LUV KASHYAP - Academia.edu (original) (raw)

Papers by LUV KASHYAP

Indian Journal of Medical Sciences, Oct 10, 2016

CONTEXT: With the completion of genome sequence of several organisms including free-living soil n... more CONTEXT: With the completion of genome sequence of several organisms including free-living soil nematode Caenorhabditis elegans, precise genome annotations of this sea of raw information are now of prime importance, as they allow the accurate definition of generic regions. Alternative splicing is seen in nearly all metazoan organisms as a means for producing functionally diverse polypeptides from a single gene. AIM: In this study, we performed a detailed and in-depth analysis of the full genomic sequence of one of the six chromosomes of C. elegans. MATERIALS AND METHODS: In this study, several bioinformatics tools including gene/exon prediction programs, ORF finders, blast analysis tools, and alignment programs were used to analyze the genes/exons encoded by chromosome 1 of C. elegans with special reference to alternatively spliced transcripts. CONCLUSION: Using these tools, we have predicted >200 new alternatively spliced hypothetical transcripts from the genes encoded by chromosome 1 in C. elegans. These new spliced transcripts were identified from unusually large untranslated (UTR) regions and large introns present at the 3' and 5' ends of the genes with a maximum number of transcripts predicted from 5' UTR analysis. Further studies and subsequent confirmation of these alternatively spliced transcripts will enhance our understanding of the genome structure, expression, and in elucidating their role during the development of C. elegans.

Journal of Visualized Experiments

Bioinformation, Oct 7, 2006

Computational gene prediction and identifying alternatively spliced isoforms have always been a c... more Computational gene prediction and identifying alternatively spliced isoforms have always been a challenging task. In this paper, we describe the performance of three gene/exon finding programmes namely Fex, Gen view2 and Gene builder capable of predicting open reading frames or exons for a given set of sequences from C. elegans genome. The predicted exons were compared with the 'sequencing consortium' identified exons and degree of consensus among them is discussed. We found that exon prediction by Fex was similar to the consortium prediction as compared to Gen view2 and Gene builder results. Interestingly, some exons (six exons in five genes) predicted positive only by Fex and not by the 'sequencing consortium' are found at the C. elegans EST database. This data is critical for further debate and discussion on gene finding in C. elegans.

<b>Copyright information:</b>Taken from "Comparative analysis of various gene fi... more <b>Copyright information:</b>Taken from "Comparative analysis of various gene finders specific to genome"Bioinformation 2006;1(6):203-207.Published online 7 Oct 2006PMCID:PMC1891687. Sequences were compared by TBLASTN computer-based sequence analysis. [] Hypothetical gene name designated by sequencing consortium is given in bold letters and amino acid sequence predicted by Fex is given next to the hypothetical gene name in bracket. Newly predicted exons were compared with cDNA sequences separately. Numbers on the left and right side of amino acid sequences indicate the position of these amino acid residues in the exons predicted by Fex (query) and cDNA hits (yk series) during TBLASTN search. Names of each cDNA clone are mentioned on the left side and their EMBL accession numbers are given on the right side of the aligned sequences.

Uncovering functional associations for genes and gene products remains one of the most significan... more Uncovering functional associations for genes and gene products remains one of the most significant challenges in biology. The classical approaches, such as homology detection, are mainly suited for predicting approximate molecular function of a protein and should be used in context with other methods. Several studies have emerged that employ knowledge-based procedures to extract functional data for genes from a variety of biological sources. However, data derived from a single biological resource often provides only a limited perspective on their functional associations largely due to systematic bias in the underlying data. The post-genomic era has witnessed the emergence of knowledge-based studies that aim to decipher functional associations by combining several biological evidence types. These are expected to provide better insights into the functional aspects of diverse genes, genomes and networks.

Computational gene prediction and identifying alternatively spliced isoforms have always been a c... more Computational gene prediction and identifying alternatively spliced isoforms have always been a challenging task. In this paper, we describe the performance of three gene/exon finding programmes namely Fex, Gen view2 and Gene builder capable of predicting open reading frames or exons for a given set of sequences from C. elegans genome. The predicted exons were compared with the ‘sequencing consortium ’ identified exons and degree of consensus among them is discussed. We found that exon prediction by Fex was similar to the consortium prediction as compared to Gen view2 and Gene builder results. Interestingly, some exons (six exons in five genes) predicted positive only by Fex and not by the ‘sequencing consortium ’ are found at the C. elegans EST database. This data is critical for further debate and discussion on gene finding in C. elegans. Key words: gene prediction; multiple transcripts; exons; isoforms; C. elegans Background: Locating and finding coding regions from a given set o...

Computational and molecular characterization of multiple isoforms of lfe-2 gene in nematode C. el... more Computational and molecular characterization of multiple isoforms of lfe-2 gene in nematode C. elegans

The sequencing of the human genome (1) has raised important questions about the nature of genomic... more The sequencing of the human genome (1) has raised important questions about the nature of genomic complexity. Scientists thought that the complex DNA of a human was made up by perhaps as many as 150,000 different genes. The approximation was based on the number of different transcripts, mRNAs, which had been found in humans, assuming that there should be one gene for each mRNA. When all the sequencing was done, the result was merely 32,000 human genes. (Later results suggest that the number is even lower, less than 25,000.) In comparison, the fruit fly Drosophila has 14,000 genes and the nematode Caenorhabditis elegans has 19,000. The report of only 32,000 human genes came as a surprise (2). The number of human expressed-sequence (mRNA) forms was much higher than the number of genes. How can the much greater size and complexity of humans be encoded in only twice the number of genes required by a fly? One way to explain this paradox is to point out that the number of possible protein...

Nitric oxide (NO) was initially described as a physiological mediator of endothelial cell relaxat... more Nitric oxide (NO) was initially described as a physiological mediator of endothelial cell relaxation, an important role in hypotension. NO is an intercellular messenger that has been recognized as one of the most versatile players in the immune system. Cells of the innate immune system--macrophages, neutrophils and natural killer cells--use pattern recognition receptors to recognize the molecular patterns associated with pathogens. Activated macrophages then inhibit pathogen replication by releasing a variety of effector molecules, including NO. In addition to macrophages, a large number of other immune-system cells produce and respond to NO. Thus, NO is important as a toxic defense molecule against infectious organisms. It also regulates the functional activity, growth and death of many immune and inflammatory cell types including macrophages, T lymphocytes, antigen-presenting cells, mast cells, neutrophils and natural killer cells. However, the role of NO in nonspecific and specif...

Nitric oxide (NO) was initially described as a physiological mediator of endothelial cell relaxat... more Nitric oxide (NO) was initially described as a physiological mediator of endothelial cell relaxation, an important role in hypotension. NO is an intercellular messenger that has been recognized as one of the most versatile players in the immune system. Cells of the innate immune system – macrophages, neutrophils and natural killer cells – use pattern recognition receptors to recognize the molecular patterns associated with pathogens. Activated macrophages then inhibit pathogen replication by releasing a variety of effector molecules, including NO. In addition to macrophages, a large number of other immune-system cells produce and respond to NO. Thus, NO is important as a toxic defense molecule against infectious organisms. It also regulates the functional activity, growth and death of many immune and inflammatory cell types including macrophages, T lymphocytes, antigen-presenting cells, mast cells, neutrophils and natural killer cells. However, the role of NO in nonspecific and spec...

Computational gene prediction and identifying alternatively spliced isoforms have always been a c... more Computational gene prediction and identifying alternatively spliced isoforms have always been a challenging task. In this paper, we describe the performance of three gene/exon finding programmes namely Fex, Gen view2 and Gene builder capable of predicting open reading frames or exons for a given set of sequences from C. elegans genome. The predicted exons were compared with the ‘sequencing consortium’ identified exons and degree of consensus among them is discussed. We found that exon prediction by Fex was similar to the consortium prediction as compared to Gen view2 and Gene builder results. Interestingly, some exons (six exons in five genes) predicted positive only by Fex and not by the ‘sequencing consortium’ are found at the C. elegans EST database. This data is critical for further debate and discussion on gene finding in C. elegans.

Indian Journal of Science and Technology

Bioinformation, Feb 1, 2006

Computational gene prediction and identifying alternatively spliced isoforms have always been a c... more Computational gene prediction and identifying alternatively spliced isoforms have always been a challenging task. In this paper, we describe the performance of three gene/exon finding programmes namely Fex, Gen view2 and Gene builder capable of predicting open reading frames or exons for a given set of sequences from C. elegans genome. The predicted exons were compared with the ‘sequencing consortium’ identified exons and degree of consensus among them is discussed. We found that exon prediction by Fex was similar to the consortium prediction as compared to Gen view2 and Gene builder results. Interestingly, some exons (six exons in five genes) predicted positive only by Fex and not by the ‘sequencing consortium’ are found at the C. elegans EST database. This data is critical for further debate and discussion on gene finding in C. elegans.

Bioinformation, Jan 7, 2006

Bioinformation, Jan 30, 2007

C. elegans C46H11.4 gene encodes a Let-23 fertility effector/regulator protein of the EGF-recepto... more C. elegans C46H11.4 gene encodes a Let-23 fertility effector/regulator protein of the EGF-receptor class of the tyrosine kinase family. Alternative splicing is a major mechanism of generating protein diversity in higher eukaryotes. C. elegans genome sequencing consortium has reported three alternatively spliced transcripts of C46H11.4 gene which encodes for three hypothetical proteins namely, C46H11.4a, C46H11.4b and C46H11.4c. Using a combination of various bioinformatics tools like gene or exon finding programmes, blast searches, alignment tools etc followed by experimental validation, we report the presence of three more alternatively spliced transcripts which encode for novel hypothetical proteins C46H11.4d, C46H11.4e and C46H11.4f. These isoforms arise as a result of alternative splicing in the pre-mRNA encoded by gene C46H11.4. These novel un-reported spliced variants not only point towards the extent of alternative splicing in C. elegans genes but also hint towards the comple...

Indian Journal of Medical Sciences, Oct 10, 2016

Journal of Visualized Experiments

Bioinformation, Oct 7, 2006

Computational gene prediction and identifying alternatively spliced isoforms have always been a c... more Computational gene prediction and identifying alternatively spliced isoforms have always been a challenging task. In this paper, we describe the performance of three gene/exon finding programmes namely Fex, Gen view2 and Gene builder capable of predicting open reading frames or exons for a given set of sequences from C. elegans genome. The predicted exons were compared with the ‘sequencing consortium ’ identified exons and degree of consensus among them is discussed. We found that exon prediction by Fex was similar to the consortium prediction as compared to Gen view2 and Gene builder results. Interestingly, some exons (six exons in five genes) predicted positive only by Fex and not by the ‘sequencing consortium ’ are found at the C. elegans EST database. This data is critical for further debate and discussion on gene finding in C. elegans. Key words: gene prediction; multiple transcripts; exons; isoforms; C. elegans Background: Locating and finding coding regions from a given set o...

Nitric oxide (NO) was initially described as a physiological mediator of endothelial cell relaxat... more Nitric oxide (NO) was initially described as a physiological mediator of endothelial cell relaxation, an important role in hypotension. NO is an intercellular messenger that has been recognized as one of the most versatile players in the immune system. Cells of the innate immune system – macrophages, neutrophils and natural killer cells – use pattern recognition receptors to recognize the molecular patterns associated with pathogens. Activated macrophages then inhibit pathogen replication by releasing a variety of effector molecules, including NO. In addition to macrophages, a large number of other immune-system cells produce and respond to NO. Thus, NO is important as a toxic defense molecule against infectious organisms. It also regulates the functional activity, growth and death of many immune and inflammatory cell types including macrophages, T lymphocytes, antigen-presenting cells, mast cells, neutrophils and natural killer cells. However, the role of NO in nonspecific and spec...

Computational gene prediction and identifying alternatively spliced isoforms have always been a c... more Computational gene prediction and identifying alternatively spliced isoforms have always been a challenging task. In this paper, we describe the performance of three gene/exon finding programmes namely Fex, Gen view2 and Gene builder capable of predicting open reading frames or exons for a given set of sequences from C. elegans genome. The predicted exons were compared with the ‘sequencing consortium’ identified exons and degree of consensus among them is discussed. We found that exon prediction by Fex was similar to the consortium prediction as compared to Gen view2 and Gene builder results. Interestingly, some exons (six exons in five genes) predicted positive only by Fex and not by the ‘sequencing consortium’ are found at the C. elegans EST database. This data is critical for further debate and discussion on gene finding in C. elegans.

Indian Journal of Science and Technology

Bioinformation, Feb 1, 2006

Computational gene prediction and identifying alternatively spliced isoforms have always been a c... more Computational gene prediction and identifying alternatively spliced isoforms have always been a challenging task. In this paper, we describe the performance of three gene/exon finding programmes namely Fex, Gen view2 and Gene builder capable of predicting open reading frames or exons for a given set of sequences from C. elegans genome. The predicted exons were compared with the ‘sequencing consortium’ identified exons and degree of consensus among them is discussed. We found that exon prediction by Fex was similar to the consortium prediction as compared to Gen view2 and Gene builder results. Interestingly, some exons (six exons in five genes) predicted positive only by Fex and not by the ‘sequencing consortium’ are found at the C. elegans EST database. This data is critical for further debate and discussion on gene finding in C. elegans.

Bioinformation, Jan 7, 2006

Bioinformation, Jan 30, 2007