Rashid Saif - Academia.edu (original) (raw)

Papers by Rashid Saif

Research paper thumbnail of Pathway enrichment and network analysis of differentially expressed genes in pashmina goat

Research paper thumbnail of Mammary tumor associated Hspb1 mutation and screening of eight cat populations of the world

Current research highlights the Hspb1 based screening of eight cat populations of the world to in... more Current research highlights the Hspb1 based screening of eight cat populations of the world to investigate the association of newly found locus within cat mammary tumors. Total 180 cats were screened on the basis of Hspb1 4 bp deletion locus (1514-1517del4) which was observed in six mammary tumor cases in Siamese cat breed. Case-control association study revealed the non-significance with P=0.201 and an overall mutant allele frequency of 0.30 ranging from 0.20-0.40 was observed in other cat populations. Similarly, HWE was also obeyed in combined population samples with P=0.860 and found non-significant with range of 0.429-0.708 in other non-Pakistani cat populations as well. These results might be helpful to understand the association of this novel locus in a better way with large sample size of cases and may also serve as a potential marker for mammary tumor diagnosis, particularly in cats and generally in all other animal populations in comparative genetics and genomics context.

Research paper thumbnail of Whole genome comparison of Pakistani Corona virus with Chinese and US strains along with its predictive severity of COVID-19

Gene Reports, Apr 15, 2021

Initially submitted 784 SARS-nCoV2 whole genome sequences on NCBI Virus database were selected fo... more Initially submitted 784 SARS-nCoV2 whole genome sequences on NCBI Virus database were selected for phylogenetic analysis to look into their similarities with two of Pakistani sequenced coronavirus strains having accessions of MT240479 and MT262993. The MT240479 named (Gilgit1-Pak) was found in close proximity to MT184913 named (CruiseA-USA), while MT262993 named (Manga-Pak) was in neighboring to MT039887 named (WI-USA) strain, which were further chosen for variant calling analysis along with reference genome NC_045512 as out-group to construct concluding cladogram and looked for evolutionary distance with PAUP software in this article. Aforementioned Pakistani strains each of having 29,836 bases were compared with MT263429 (WI-USA) of 29,889 bases and MT259229 (Wuhan-P.R. China) of 29,864 bases. Whole genome variant calling pipeline revealed 31 variants in both Pakistani strains collectively (Manga-Pak vs USA having 2del & 7SNPs, while different from Chinese strain with 2del & 2SNPs...

Research paper thumbnail of Computational prediction of Carica papaya extracts as potential drug agents against RNA polymerase and Spike proteins of SARS-nCoV2

The emergence of COVID-19 outbreak caused by SARS-nCoV2 (Severe Acute Respiratory Syndrome novel ... more The emergence of COVID-19 outbreak caused by SARS-nCoV2 (Severe Acute Respiratory Syndrome novel coronavirus 2), lead to the mass-scale mortalities around the world within a short span of time. The hour of the need is to develop the strategies and designing drugs/vaccines to control the spread of this contagion. In this paper, we predict the promising drug agents from the Carica papaya compounds by docking them with two major drug target proteins of SARS-nCoV2, spike (7BZ5) and RNA-dependent RNA polymerase (7BW4). For this purpose, we used Molecular Operating Environment Software (MOE) for ligand-protein interactions and docking scores. Furthermore, we used PubChem, PDB and SwissADME web portals to retrieve ligands structures, proteins structures and to check Lipinski’s physiochemical parameters respectively. Cumulatively, this docking study has shown significant binding energies that (-4.2034 to -8.9013 Kcal/mol) indicates their potential against COVID-19 treatment. This study need...

Research paper thumbnail of Introduction to Galaxy Platform for NGS Variant Calling Pipeline

Advancements in Life Sciences, 2020

Background: Galaxy web-based platform for Next Generation Sequence (NGS) data analysis provides ... more Background: Galaxy web-based platform for Next Generation Sequence (NGS) data analysis provides unprecedented opportunities to characterize, analyze and computationally visualize genomic landscapes with limited-resources. An initiative was taken to explore this pipeline for NGS data-analysis by using Galaxy platform, for its relative accessibility, reproducibility, transparency and scalability. Methods: Variant calling and associated workflows were executed on NGS pooled-seq data of 12 Pakistani Teddy goats. Different tools used in this pipeline are FastQC for quality checks, Trimmomatic for trimming data, SAM/BAM tools for conversion of file formats, Picard tools for marking deduplicates, VCFtools/FreeBayes for genomic variant detection and SnpSift to annotate the variants. Results: Highly associated functionally untrivial 43,712 loci were percolated having 87,510 alleles. Besides, 1,548 variants with 1,134 SNPs, 23 mixed variants, 76 MNP, 183 insertions and 132 deletions were...

Research paper thumbnail of Molecular Characterization of EGLN 1 Gene in Fast and Slow Moving Animals of Diverse Terrain

ackground: Process of animal migration from their habitat to a new environment is always problema... more ackground: Process of animal migration from their habitat to a new environment is always problematic due to low adaptive tendency, which ultimately affect their production, behavior and overall performance. Current study is focused to explore the sequence diversity of EGLN1 gene in relation to animal acclimatization at higher altitude under deprived oxygen or ability of better utilization of oxygen which is considered to be liable for their agility in diverse terrains. Fast and slow moving animals of plain and hilly terrains are potential species to study this phenomenon.

Research paper thumbnail of First Step with R for Life Sciences: Learning Basics of this Tool for NGS Data Analysis

Advancements in Life Sciences, 2019

Background: R is one of the renowned programming language which is an open source software devel... more Background: R is one of the renowned programming language which is an open source software developed by the scientific community to compute, analyze and visualize big data of any field including biomedical research for bioinformatics applications. Methods: Here, we outlined R allied packages and affiliated bioinformatics infrastructures e.g. Bioconductor and CRAN. Moreover, basic concepts of factor, vector, data matrix and whole transcriptome RNA-Seq data was analyzed and discussed. Particularly, differential expression workflow on simulated prostate cancer RNA-Seq data was performed through experimental design, data normalization, hypothesis testing and downstream investigations using EdgeR package. A few genes with ectopic expression were retrieved and knowhow to gene enrichment pathway analysis is highlighted using available online tools. Results: Data matrix of (4×3) was constructed, and a complex data matrix of Golub et al ., was analyzed through χ2 statistics by generating...

Research paper thumbnail of Dog Coat Colour Genetics: A Review

anis lupus familiaris is one of the most beloved pet species with hundreds of world-wide recogniz... more anis lupus familiaris is one of the most beloved pet species with hundreds of world-wide recognized breeds, which can be differentiated from each other by specific morphological, behavioral and adoptive traits. Morphological characteristics of dog breeds get more attention which can be defined mostly by coat color and its texture, and considered to be incredibly lucrative traits in this valued species. Although the genetic foundation of coat color has been well stated in the literature, but still very little is known about the growth pattern, hair length and curly coat trait genes. Skin pigmentation is determined by eumelanin and pheomelanin switching phenomenon which is under the control of Melanocortin 1 Receptor and Agouti Signaling Protein genes. Genetic variations in the genes involved in pigmentation pathway provide basic understanding of melanocortin physiology and evolutionary adaptation of this trait. So in this review, we highlighted, gathered and comprehend the genetic mu...

Research paper thumbnail of Single nucleotide somatic variants of Tp53 gene in widespread neoplasms of Canis Familiaris

Journal of Animal and Plant Sciences, 2018

Sequence diversity of Tp53 gene was analyzed in dog tumors to have an insight of accumulated soma... more Sequence diversity of Tp53 gene was analyzed in dog tumors to have an insight of accumulated somatic mutations in 18 samples belongs to 7 different types of cancers. Nine different polymorphic sites were observed in exon 3, 4 and 5, while 32 polymorphic sites are observed in intron 3, 4 and 9. Most of these alterations are heterozygous, locus c.76 in exon 3 is transversion with homozygous (G) variant in one of the mammary and CTVT samples, which is missense in nature and alter the leucine amino acid to valine. Similarly, c.356 locus in exon 5 is homozygous (C), that is also a transversion, which changed the lysine residue to threonine. Most of the observed cancer samples are heterozygous in intronic regions of this gene. Current study of sequence variations of cancerous somatic cells in the aforementioned gene confirm the involvement of this gene in cancer pathways and might serve as potential molecular diagnostic and prognostic marker for these cancer types in Canis familiaris and ...

Research paper thumbnail of Sequence Diversity of MAOA Gene within Wild and Docile Animal Species

Advancements in Life Sciences, 2018

Background: Molecular characterization of MAOA gene was performed to investigate aggressive beh... more Background: Molecular characterization of MAOA gene was performed to investigate aggressive behaviour within wild (lion, leopard, and wolf) as opposed to docile animal (sheep, goat) species living in different habitats, by undertaking sequence diversity analysis of this gene. Methods: The MAOA gene was partially amplified by PCR for wild and docile animal species. Amplified DNA was sequenced and then analyzed using BioEdit and Sequencher softwares, while multiple sequence alignment and phylogenetics analysis were conducted through MEGA software. Bioinformatics tool like Prosite scan, Motif Scan and Prot Param were used to study properties of mutant proteins of MAOA gene. Results: Different polymorphic sites were observed which included c.956, c.1063 in docile animals and c.2530 in wild animals. Phylogenetic analysis based on this candidate gene endorsed the existing taxonomy of subject animals, while bioinformatics tools explored the altered characteristics of mutant MAOA pr...

Research paper thumbnail of Insight of Tp53 Mutations and their effect on Protein in Different Feline and Canine Neoplasms

Advancements in Life Sciences, 2016

Background : Mutations in the Tp53 gene, a tumor suppressor gene, may cause dysfunction in gro... more Background : Mutations in the Tp53 gene, a tumor suppressor gene, may cause dysfunction in growing cells and hinder the phenomenon of apoptosis, an alleged cause of tumorigenesis. It is involved in conservation of the genome and DNA repair, mutations of this gene may cause the damaged cells to grow continuously. Methods: The type of molecular changes in Tp53 gene and their effects on physiochemical and structural properties of this protein in various Canine and Feline cancers were observed in this study by using online bioinformatics tools. Results: Our results indicated that lymphomas and perianal adenocarcinomas (PAC) have the same mutation at c. 104, while mammary tumors and canine transmissible venereal tumor (CTVT) contain different mutations. Referring to changes in protein, synonymous mutations in granulomas were observed while certain mutations in squamous cell carcinoma (SCC) and head & neck tumors were detected in Canis familiaris . In Felis catus , the mutant...

Research paper thumbnail of Genomic exploration of Pakistani buffalo - our black gold

Research paper thumbnail of Differential Gene Expression Pipeline for Whole Transcriptome RNA-Seq Data using Personal Computer

Advances in the next generation sequencing (NGS) technologies, their cost effectiveness and well-... more Advances in the next generation sequencing (NGS) technologies, their cost effectiveness and well-developed pipelines using computational tools/softwares has allowed researchers to reveal ground-breaking discoveries in multi-omics data analysis. However, there is still uncertainty due to massive upsurge in parallel tools and difficulty in choosing best practiced pipeline for expression profiling of RNA sequenced (RNA-seq) data. Here, we detail the optimized pipeline that works at a fast pace with enhanced accuracy on personal computer rather than using cloud or high-performance computing clusters (HPC). The steps include quality check, base filtration, quasi-mapping, quantification of samples, estimation and counting of transcript/gene expression abundances, identification and clustering of differentially expressed features and visualization of the data. The tools FastQC, Trimmomatic, Salmon and some other scripts in Trinity toolkit were applied on two paired-end datasets. An extensi...

Research paper thumbnail of Mathematical Understanding of Sequence Alignment and Phylogenetic Algorithms: A Comprehensive Review of Methods

Context: Pairwise sequence alignment is one of the ways to arrange two biological sequences to id... more Context: Pairwise sequence alignment is one of the ways to arrange two biological sequences to identify regions of resemblance that may suggest the functional, structural, and/or evolutionary relationship (proteins or nucleic acids) between the sequences. There are two strategies in pairwise sequence alignment: Local sequence Alignment (Smith-waterman algorithm) and Global sequence Alignment (Needleman-Wunsch algorithm). In local sequence alignment, two sequences that may or may not be related are aligned to find regions of local similarities in large sequences whereas in global sequence alignment, two sequences same in length are aligned to identify conserved regions. Similarities and divergence between biological sequences identified by sequence alignment also have to be rationalized and visualized in the sense of phylogenetic trees. The phylogenetic tree construction methods are divided into distance-based and characterbased methods. Evidence Acquisition: In this article, differe...

Research paper thumbnail of Glyphosate: cancerous or not? Perspectives from both ends of the debate

Glyphosate is non-selective herbicide. Studies published in the last decade, point towards glypho... more Glyphosate is non-selective herbicide. Studies published in the last decade, point towards glyphosate toxicity. Shikimic acid pathway for the biosynthesis of folates and aromatic amino acids is inhibited by glyphosate. Glyphosate carcinogenicity is still considered to be a controversial issue. The World Health Organizations’ International Agency recently concluded that glyphosate is “probably carcinogenic to humans.” Some researchers believed that glyphosate is not linked with carcinogenicity.

Research paper thumbnail of Whole-Genome Selective Sweeps Analysis in Pakistani Kamori Goat

Research paper thumbnail of Why Pashmina Goat Produces Long Hair-fiber and Barbari doesn’t: A Differential Gene Expression Study

The Pashmina and Barbari are two famous goat breeds found in the wide areas of the Indo-Pak regio... more The Pashmina and Barbari are two famous goat breeds found in the wide areas of the Indo-Pak region. Pashmina is famous for its long hair-fiber (Cashmere) production while Barbari is not-selected for this trait. So, the mRNA expression profiling in the skin samples of both breeds would be an attractive and judicious approach for detecting putative genes involved in this valued trait. Here, we performed differential gene expression analysis on publicly available RNA-Seq data from both breeds. Out of 44,617,994 filtered reads of Pashmina and 55,995,999 of Barbari which are 76.48% and 73.69% mapped to the ARS1 reference transcriptome assembly respectively. A Pairwise comparison of both breeds resulted in 47,159 normalized expressed transcripts while 8,414 transcripts are differentially expressed above the significant threshold. Among these, 4,788 are upregulated in Pashmina while 3,626 transcripts are upregulated in Barbari. Fifty-nine transcripts harbor 57 genes including 32 LOC genes ...

Research paper thumbnail of Use of CO1 gene sequences for computing genetic diversity between Cirrhinus mrigala from two different habitats (Farm and River)

DNA barcoding technique involving documentation of animal species based on a partial sequence of ... more DNA barcoding technique involving documentation of animal species based on a partial sequence of cytochrome C Oxidase 1 gene from mitochondrial DNA attracted many scientists at the start of 21 century. The flaws in morphometric methods for identification of larvae of fishes and other animals, their eggs, and damaged specimen with incomplete morphology upraised the question for an alternate method for identification and grouping of many animal species. Partial sequence of CO1 gene used as barcode has been attested as a valuable tool for identification of fish species as well as supportive in computing evolutionary history and genetic diversity. Current study was conducted to identify the fishes by using the DNA barcoding technique resulting partial sequences of CO1 gene, and then use of these sequences in evaluation of the evolutionary history and genetic diversity of Cirrhinus mrigala inhabiting different areas. Short sequences from 5 end of CO1 gene (650 base pair) were amplified, ...

Research paper thumbnail of An Overview of Genome-Wide Association Study for Genetics Novices: A Review

SNP chip-based genome-wide association studies (GWAS) is an inspiring and fast scanning method fo... more SNP chip-based genome-wide association studies (GWAS) is an inspiring and fast scanning method for mapping variations within the genome and associating them with specific diseases/trait. This association information has enhanced the chances of improvement in disease diagnosis, understanding the causative variants locations and associated gene hunting strategies. GWAS have laid foundation of an era in which both personalized medicine and pharmacogenomics would be reinforced along with better understanding of functional genomics aspects of modern molecular genetics. Since the advent of first GWAS in 2002, thousands of genome wide association studies have been published which have proven GWAS a successful methodology in identifying significant variants in disease/trait association but application of GWAS outcomes to clinical settings demands more evaluation for validity. Here, we have divided the GWAS approach into various aspects including history, development, analysis strategies, ap...

Research paper thumbnail of Computational Prediction of Olea europaea Compounds as Inhibitor of Main-Peptidase of SARS-CoV2

Background: In December 2019, Severe Acute Respiratory Syndrome Novel Coronavirus 2 (SARS-nCOV2) ... more Background: In December 2019, Severe Acute Respiratory Syndrome Novel Coronavirus 2 (SARS-nCOV2) was identified as potential causative agent for COVID-19 in the Wuhan City of China. This disease spread around the whole globe, thus WHO declared it as a pandemic by March 11, 2020. Due to rapid mutation rate, lack of specific genomic knowledge and treatment modalities against this RNA based virus, world scientific community urges to work for vaccine production, treatments options and alternative remedies including eastern herbs as potential anti-viral agents. Methods: Olea europaea (Olive) was found highly beneficial on the basis of its previous therapeutic applications. So, in the current study, its five different compounds (Catechin, Cynaroside, Elenolic Acid, Hydroxytyrosol, and Oleuropein) were chosen according to Lipinski physiochemical parameters, which were compared with already clinically used five anti-viral drugs (Ribavirin, Niclosamide, Nelfinavir, S-Nitroso-N-acetyl penicil...

Research paper thumbnail of Pathway enrichment and network analysis of differentially expressed genes in pashmina goat

Research paper thumbnail of Mammary tumor associated Hspb1 mutation and screening of eight cat populations of the world

Current research highlights the Hspb1 based screening of eight cat populations of the world to in... more Current research highlights the Hspb1 based screening of eight cat populations of the world to investigate the association of newly found locus within cat mammary tumors. Total 180 cats were screened on the basis of Hspb1 4 bp deletion locus (1514-1517del4) which was observed in six mammary tumor cases in Siamese cat breed. Case-control association study revealed the non-significance with P=0.201 and an overall mutant allele frequency of 0.30 ranging from 0.20-0.40 was observed in other cat populations. Similarly, HWE was also obeyed in combined population samples with P=0.860 and found non-significant with range of 0.429-0.708 in other non-Pakistani cat populations as well. These results might be helpful to understand the association of this novel locus in a better way with large sample size of cases and may also serve as a potential marker for mammary tumor diagnosis, particularly in cats and generally in all other animal populations in comparative genetics and genomics context.

Research paper thumbnail of Whole genome comparison of Pakistani Corona virus with Chinese and US strains along with its predictive severity of COVID-19

Gene Reports, Apr 15, 2021

Initially submitted 784 SARS-nCoV2 whole genome sequences on NCBI Virus database were selected fo... more Initially submitted 784 SARS-nCoV2 whole genome sequences on NCBI Virus database were selected for phylogenetic analysis to look into their similarities with two of Pakistani sequenced coronavirus strains having accessions of MT240479 and MT262993. The MT240479 named (Gilgit1-Pak) was found in close proximity to MT184913 named (CruiseA-USA), while MT262993 named (Manga-Pak) was in neighboring to MT039887 named (WI-USA) strain, which were further chosen for variant calling analysis along with reference genome NC_045512 as out-group to construct concluding cladogram and looked for evolutionary distance with PAUP software in this article. Aforementioned Pakistani strains each of having 29,836 bases were compared with MT263429 (WI-USA) of 29,889 bases and MT259229 (Wuhan-P.R. China) of 29,864 bases. Whole genome variant calling pipeline revealed 31 variants in both Pakistani strains collectively (Manga-Pak vs USA having 2del & 7SNPs, while different from Chinese strain with 2del & 2SNPs...

Research paper thumbnail of Computational prediction of Carica papaya extracts as potential drug agents against RNA polymerase and Spike proteins of SARS-nCoV2

The emergence of COVID-19 outbreak caused by SARS-nCoV2 (Severe Acute Respiratory Syndrome novel ... more The emergence of COVID-19 outbreak caused by SARS-nCoV2 (Severe Acute Respiratory Syndrome novel coronavirus 2), lead to the mass-scale mortalities around the world within a short span of time. The hour of the need is to develop the strategies and designing drugs/vaccines to control the spread of this contagion. In this paper, we predict the promising drug agents from the Carica papaya compounds by docking them with two major drug target proteins of SARS-nCoV2, spike (7BZ5) and RNA-dependent RNA polymerase (7BW4). For this purpose, we used Molecular Operating Environment Software (MOE) for ligand-protein interactions and docking scores. Furthermore, we used PubChem, PDB and SwissADME web portals to retrieve ligands structures, proteins structures and to check Lipinski’s physiochemical parameters respectively. Cumulatively, this docking study has shown significant binding energies that (-4.2034 to -8.9013 Kcal/mol) indicates their potential against COVID-19 treatment. This study need...

Research paper thumbnail of Introduction to Galaxy Platform for NGS Variant Calling Pipeline

Advancements in Life Sciences, 2020

Background: Galaxy web-based platform for Next Generation Sequence (NGS) data analysis provides ... more Background: Galaxy web-based platform for Next Generation Sequence (NGS) data analysis provides unprecedented opportunities to characterize, analyze and computationally visualize genomic landscapes with limited-resources. An initiative was taken to explore this pipeline for NGS data-analysis by using Galaxy platform, for its relative accessibility, reproducibility, transparency and scalability. Methods: Variant calling and associated workflows were executed on NGS pooled-seq data of 12 Pakistani Teddy goats. Different tools used in this pipeline are FastQC for quality checks, Trimmomatic for trimming data, SAM/BAM tools for conversion of file formats, Picard tools for marking deduplicates, VCFtools/FreeBayes for genomic variant detection and SnpSift to annotate the variants. Results: Highly associated functionally untrivial 43,712 loci were percolated having 87,510 alleles. Besides, 1,548 variants with 1,134 SNPs, 23 mixed variants, 76 MNP, 183 insertions and 132 deletions were...

Research paper thumbnail of Molecular Characterization of EGLN 1 Gene in Fast and Slow Moving Animals of Diverse Terrain

ackground: Process of animal migration from their habitat to a new environment is always problema... more ackground: Process of animal migration from their habitat to a new environment is always problematic due to low adaptive tendency, which ultimately affect their production, behavior and overall performance. Current study is focused to explore the sequence diversity of EGLN1 gene in relation to animal acclimatization at higher altitude under deprived oxygen or ability of better utilization of oxygen which is considered to be liable for their agility in diverse terrains. Fast and slow moving animals of plain and hilly terrains are potential species to study this phenomenon.

Research paper thumbnail of First Step with R for Life Sciences: Learning Basics of this Tool for NGS Data Analysis

Advancements in Life Sciences, 2019

Background: R is one of the renowned programming language which is an open source software devel... more Background: R is one of the renowned programming language which is an open source software developed by the scientific community to compute, analyze and visualize big data of any field including biomedical research for bioinformatics applications. Methods: Here, we outlined R allied packages and affiliated bioinformatics infrastructures e.g. Bioconductor and CRAN. Moreover, basic concepts of factor, vector, data matrix and whole transcriptome RNA-Seq data was analyzed and discussed. Particularly, differential expression workflow on simulated prostate cancer RNA-Seq data was performed through experimental design, data normalization, hypothesis testing and downstream investigations using EdgeR package. A few genes with ectopic expression were retrieved and knowhow to gene enrichment pathway analysis is highlighted using available online tools. Results: Data matrix of (4×3) was constructed, and a complex data matrix of Golub et al ., was analyzed through χ2 statistics by generating...

Research paper thumbnail of Dog Coat Colour Genetics: A Review

anis lupus familiaris is one of the most beloved pet species with hundreds of world-wide recogniz... more anis lupus familiaris is one of the most beloved pet species with hundreds of world-wide recognized breeds, which can be differentiated from each other by specific morphological, behavioral and adoptive traits. Morphological characteristics of dog breeds get more attention which can be defined mostly by coat color and its texture, and considered to be incredibly lucrative traits in this valued species. Although the genetic foundation of coat color has been well stated in the literature, but still very little is known about the growth pattern, hair length and curly coat trait genes. Skin pigmentation is determined by eumelanin and pheomelanin switching phenomenon which is under the control of Melanocortin 1 Receptor and Agouti Signaling Protein genes. Genetic variations in the genes involved in pigmentation pathway provide basic understanding of melanocortin physiology and evolutionary adaptation of this trait. So in this review, we highlighted, gathered and comprehend the genetic mu...

Research paper thumbnail of Single nucleotide somatic variants of Tp53 gene in widespread neoplasms of Canis Familiaris

Journal of Animal and Plant Sciences, 2018

Sequence diversity of Tp53 gene was analyzed in dog tumors to have an insight of accumulated soma... more Sequence diversity of Tp53 gene was analyzed in dog tumors to have an insight of accumulated somatic mutations in 18 samples belongs to 7 different types of cancers. Nine different polymorphic sites were observed in exon 3, 4 and 5, while 32 polymorphic sites are observed in intron 3, 4 and 9. Most of these alterations are heterozygous, locus c.76 in exon 3 is transversion with homozygous (G) variant in one of the mammary and CTVT samples, which is missense in nature and alter the leucine amino acid to valine. Similarly, c.356 locus in exon 5 is homozygous (C), that is also a transversion, which changed the lysine residue to threonine. Most of the observed cancer samples are heterozygous in intronic regions of this gene. Current study of sequence variations of cancerous somatic cells in the aforementioned gene confirm the involvement of this gene in cancer pathways and might serve as potential molecular diagnostic and prognostic marker for these cancer types in Canis familiaris and ...

Research paper thumbnail of Sequence Diversity of MAOA Gene within Wild and Docile Animal Species

Advancements in Life Sciences, 2018

Background: Molecular characterization of MAOA gene was performed to investigate aggressive beh... more Background: Molecular characterization of MAOA gene was performed to investigate aggressive behaviour within wild (lion, leopard, and wolf) as opposed to docile animal (sheep, goat) species living in different habitats, by undertaking sequence diversity analysis of this gene. Methods: The MAOA gene was partially amplified by PCR for wild and docile animal species. Amplified DNA was sequenced and then analyzed using BioEdit and Sequencher softwares, while multiple sequence alignment and phylogenetics analysis were conducted through MEGA software. Bioinformatics tool like Prosite scan, Motif Scan and Prot Param were used to study properties of mutant proteins of MAOA gene. Results: Different polymorphic sites were observed which included c.956, c.1063 in docile animals and c.2530 in wild animals. Phylogenetic analysis based on this candidate gene endorsed the existing taxonomy of subject animals, while bioinformatics tools explored the altered characteristics of mutant MAOA pr...

Research paper thumbnail of Insight of Tp53 Mutations and their effect on Protein in Different Feline and Canine Neoplasms

Advancements in Life Sciences, 2016

Background : Mutations in the Tp53 gene, a tumor suppressor gene, may cause dysfunction in gro... more Background : Mutations in the Tp53 gene, a tumor suppressor gene, may cause dysfunction in growing cells and hinder the phenomenon of apoptosis, an alleged cause of tumorigenesis. It is involved in conservation of the genome and DNA repair, mutations of this gene may cause the damaged cells to grow continuously. Methods: The type of molecular changes in Tp53 gene and their effects on physiochemical and structural properties of this protein in various Canine and Feline cancers were observed in this study by using online bioinformatics tools. Results: Our results indicated that lymphomas and perianal adenocarcinomas (PAC) have the same mutation at c. 104, while mammary tumors and canine transmissible venereal tumor (CTVT) contain different mutations. Referring to changes in protein, synonymous mutations in granulomas were observed while certain mutations in squamous cell carcinoma (SCC) and head & neck tumors were detected in Canis familiaris . In Felis catus , the mutant...

Research paper thumbnail of Genomic exploration of Pakistani buffalo - our black gold

Research paper thumbnail of Differential Gene Expression Pipeline for Whole Transcriptome RNA-Seq Data using Personal Computer

Advances in the next generation sequencing (NGS) technologies, their cost effectiveness and well-... more Advances in the next generation sequencing (NGS) technologies, their cost effectiveness and well-developed pipelines using computational tools/softwares has allowed researchers to reveal ground-breaking discoveries in multi-omics data analysis. However, there is still uncertainty due to massive upsurge in parallel tools and difficulty in choosing best practiced pipeline for expression profiling of RNA sequenced (RNA-seq) data. Here, we detail the optimized pipeline that works at a fast pace with enhanced accuracy on personal computer rather than using cloud or high-performance computing clusters (HPC). The steps include quality check, base filtration, quasi-mapping, quantification of samples, estimation and counting of transcript/gene expression abundances, identification and clustering of differentially expressed features and visualization of the data. The tools FastQC, Trimmomatic, Salmon and some other scripts in Trinity toolkit were applied on two paired-end datasets. An extensi...

Research paper thumbnail of Mathematical Understanding of Sequence Alignment and Phylogenetic Algorithms: A Comprehensive Review of Methods

Context: Pairwise sequence alignment is one of the ways to arrange two biological sequences to id... more Context: Pairwise sequence alignment is one of the ways to arrange two biological sequences to identify regions of resemblance that may suggest the functional, structural, and/or evolutionary relationship (proteins or nucleic acids) between the sequences. There are two strategies in pairwise sequence alignment: Local sequence Alignment (Smith-waterman algorithm) and Global sequence Alignment (Needleman-Wunsch algorithm). In local sequence alignment, two sequences that may or may not be related are aligned to find regions of local similarities in large sequences whereas in global sequence alignment, two sequences same in length are aligned to identify conserved regions. Similarities and divergence between biological sequences identified by sequence alignment also have to be rationalized and visualized in the sense of phylogenetic trees. The phylogenetic tree construction methods are divided into distance-based and characterbased methods. Evidence Acquisition: In this article, differe...

Research paper thumbnail of Glyphosate: cancerous or not? Perspectives from both ends of the debate

Glyphosate is non-selective herbicide. Studies published in the last decade, point towards glypho... more Glyphosate is non-selective herbicide. Studies published in the last decade, point towards glyphosate toxicity. Shikimic acid pathway for the biosynthesis of folates and aromatic amino acids is inhibited by glyphosate. Glyphosate carcinogenicity is still considered to be a controversial issue. The World Health Organizations’ International Agency recently concluded that glyphosate is “probably carcinogenic to humans.” Some researchers believed that glyphosate is not linked with carcinogenicity.

Research paper thumbnail of Whole-Genome Selective Sweeps Analysis in Pakistani Kamori Goat

Research paper thumbnail of Why Pashmina Goat Produces Long Hair-fiber and Barbari doesn’t: A Differential Gene Expression Study

The Pashmina and Barbari are two famous goat breeds found in the wide areas of the Indo-Pak regio... more The Pashmina and Barbari are two famous goat breeds found in the wide areas of the Indo-Pak region. Pashmina is famous for its long hair-fiber (Cashmere) production while Barbari is not-selected for this trait. So, the mRNA expression profiling in the skin samples of both breeds would be an attractive and judicious approach for detecting putative genes involved in this valued trait. Here, we performed differential gene expression analysis on publicly available RNA-Seq data from both breeds. Out of 44,617,994 filtered reads of Pashmina and 55,995,999 of Barbari which are 76.48% and 73.69% mapped to the ARS1 reference transcriptome assembly respectively. A Pairwise comparison of both breeds resulted in 47,159 normalized expressed transcripts while 8,414 transcripts are differentially expressed above the significant threshold. Among these, 4,788 are upregulated in Pashmina while 3,626 transcripts are upregulated in Barbari. Fifty-nine transcripts harbor 57 genes including 32 LOC genes ...

Research paper thumbnail of Use of CO1 gene sequences for computing genetic diversity between Cirrhinus mrigala from two different habitats (Farm and River)

DNA barcoding technique involving documentation of animal species based on a partial sequence of ... more DNA barcoding technique involving documentation of animal species based on a partial sequence of cytochrome C Oxidase 1 gene from mitochondrial DNA attracted many scientists at the start of 21 century. The flaws in morphometric methods for identification of larvae of fishes and other animals, their eggs, and damaged specimen with incomplete morphology upraised the question for an alternate method for identification and grouping of many animal species. Partial sequence of CO1 gene used as barcode has been attested as a valuable tool for identification of fish species as well as supportive in computing evolutionary history and genetic diversity. Current study was conducted to identify the fishes by using the DNA barcoding technique resulting partial sequences of CO1 gene, and then use of these sequences in evaluation of the evolutionary history and genetic diversity of Cirrhinus mrigala inhabiting different areas. Short sequences from 5 end of CO1 gene (650 base pair) were amplified, ...

Research paper thumbnail of An Overview of Genome-Wide Association Study for Genetics Novices: A Review

SNP chip-based genome-wide association studies (GWAS) is an inspiring and fast scanning method fo... more SNP chip-based genome-wide association studies (GWAS) is an inspiring and fast scanning method for mapping variations within the genome and associating them with specific diseases/trait. This association information has enhanced the chances of improvement in disease diagnosis, understanding the causative variants locations and associated gene hunting strategies. GWAS have laid foundation of an era in which both personalized medicine and pharmacogenomics would be reinforced along with better understanding of functional genomics aspects of modern molecular genetics. Since the advent of first GWAS in 2002, thousands of genome wide association studies have been published which have proven GWAS a successful methodology in identifying significant variants in disease/trait association but application of GWAS outcomes to clinical settings demands more evaluation for validity. Here, we have divided the GWAS approach into various aspects including history, development, analysis strategies, ap...

Research paper thumbnail of Computational Prediction of Olea europaea Compounds as Inhibitor of Main-Peptidase of SARS-CoV2

Background: In December 2019, Severe Acute Respiratory Syndrome Novel Coronavirus 2 (SARS-nCOV2) ... more Background: In December 2019, Severe Acute Respiratory Syndrome Novel Coronavirus 2 (SARS-nCOV2) was identified as potential causative agent for COVID-19 in the Wuhan City of China. This disease spread around the whole globe, thus WHO declared it as a pandemic by March 11, 2020. Due to rapid mutation rate, lack of specific genomic knowledge and treatment modalities against this RNA based virus, world scientific community urges to work for vaccine production, treatments options and alternative remedies including eastern herbs as potential anti-viral agents. Methods: Olea europaea (Olive) was found highly beneficial on the basis of its previous therapeutic applications. So, in the current study, its five different compounds (Catechin, Cynaroside, Elenolic Acid, Hydroxytyrosol, and Oleuropein) were chosen according to Lipinski physiochemical parameters, which were compared with already clinically used five anti-viral drugs (Ribavirin, Niclosamide, Nelfinavir, S-Nitroso-N-acetyl penicil...