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GENOME-WIDE DETECTION OF ALTERNATIVE SPLICING IN EXPRESSED SEQUENCES USING PARTIAL ORDER MULTIPLE SEQUENCE ALIGNMENT GRAPHS

C. GRASSO, B. MODREK, Y. XING, C. LEE
2003 Biocomputing 2004  
We present a method for high-throughput alternative splicing detection in expressed sequence data.  ...  for the real complexity of expressed sequence data by building and analyzing a single multiple sequence alignment containing all of the expressed sequences in a particular cluster aligned to genomic sequence  ...  Discussion and conclusions We have presented a method for genome-wide detection of splicing and alternative splicing using expressed sequence data.  ... 
doi:10.1142/9789812704856_0004 fatcat:pnniwrkgmbenpf5efdefv5lmdy

Genome-wide detection of alternative splicing in expressed sequences of human genes

B. Modrek
2001 Nucleic Acids Research  
We present a method for high-throughput alternative splicing detection in expressed sequence data.  ...  for the real complexity of expressed sequence data by building and analyzing a single multiple sequence alignment containing all of the expressed sequences in a particular cluster aligned to genomic sequence  ...  Discussion and conclusions We have presented a method for genome-wide detection of splicing and alternative splicing using expressed sequence data.  ... 
doi:10.1093/nar/29.13.2850 pmid:11433032 pmcid:PMC55780 fatcat:xlmy2izienhczbvlxv7absqmdy

Bioinformatics analysis of alternative splicing

C. Lee
2005 Briefings in Bioinformatics  
Comparative genomics studies in both mammals and insects have demonstrated that alternative splicing can in some cases be predicted directly from comparisons of genome sequences, based on heightened sequence  ...  Over the past few years, the analysis of alternative splicing using bioinformatics has emerged as an important new field, and has significantly changed our view of genome function.  ...  EST strings fuse to form a directed graph like that of partial order alignment.  ... 
doi:10.1093/bib/6.1.23 pmid:15826354 fatcat:6abvovvbwvdgfnn374o2glirju

Statistical and Computational Methods for High-Throughput Sequencing Data Analysis of Alternative Splicing

Liang Chen
2012 Statistics in Biosciences  
On the other hand, splice junction reads play an important role in the detection and quantification of alternative splicing events because they provide the direct evidence of exon-exon joining events.  ...  Here we discuss methods in splice junction read mapping, and methods in exon-centric or isoform-centric quantification of alternative splicing.  ...  Chen is supported in part by the NIH Grant R01GM097230.  ... 
doi:10.1007/s12561-012-9064-7 pmid:24058384 pmcid:PMC3776476 fatcat:q65pjjb5c5bsbp43ebhe2g7jbq

The Multiassembly Problem: Reconstructing Multiple Transcript Isoforms From EST Fragment Mixtures

Y. Xing
2004 Genome Research  
Using this algorithm, we have constructed an Alternatively Spliced Proteins database (ASP) from analysis of human expressed and genomic sequences, consisting of 13,384 protein isoforms of 4422 genes, yielding  ...  Recent evidence of abundant transcript variation (e.g., alternative splicing, alternative initiation, alternative polyadenylation) in complex genomes indicates that cataloging the complete set of transcripts  ...  Alternative Splicing Analysis Our algorithm begins with partial order alignment of expressed sequences to genomic sequence using the program POA, and identification of splices observed as gaps within each  ... 
doi:10.1101/gr.1304504 pmid:14962984 pmcid:PMC353230 fatcat:ujgmvlcrmzcyfaq7xhrwbddshe

Generating consensus sequences from partial order multiple sequence alignment graphs

C. Lee
2003 Bioinformatics  
Results: Partial Order Alignment (POA) enables construction and analysis of multiple sequence alignments as directed acyclic graphs containing complex branching structure.  ...  We illustrate its value for analyzing expressed sequence alignments to detect alternative splicing, reconstruct full length mRNA isoform sequences from EST fragments, and separate paralog mixtures that  ...  Department of Energy grant DEFG0387ER60615.  ... 
doi:10.1093/bioinformatics/btg109 pmid:12761063 fatcat:vme7737mtfbnpgkifyclxc6twa

Transcriptomic Profiling Using Next Generation Sequencing - Advances, Advantages, and Challenges [chapter]

Krishanpal Anamika, Srikant Verma, Abhay Jere, Aarti Desai
2016 Next Generation Sequencing - Advances, Applications and Challenges  
RNA Sequencing (RNASeq) is one of the latest techniques applied to study genome-wide transcriptome characterization and profiling using high-throughput sequenced data.  ...  Each of these RNA molecules plays a vital role in the physiological response, and understanding the regulation of these molecules is extremely critical for the better understanding of the functional genome  ...  In the case of RNASeq data, occurrence of large bubbles and open-ended branches in the graph suggests presence of alternative splicing and alternative transcription start and end.  ... 
doi:10.5772/61789 fatcat:psftl6dwxnc6rpxq6ho2jqz7ru

A Method for Isoform Prediction from RNA-Seq Data by Iterative Mapping

Tomoshige Ohno, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda
2012 IPSJ Transactions on Bioinformatics  
Conventional RNA-Seq analysis methods typically align reads onto a reference genome (mapping) in order to capture the form of isoforms that each gene yields and how much of every isoform is expressed from  ...  Alternative splicing plays an important role in eukaryotic gene expression by producing diverse proteins from a single gene. Predicting how genes are transcribed is of great biological interest.  ...  This work was partially supported by Grants-in-Aid for Scientific Research (22680023 and 22310125) from JSPS, and by SPIRE Supercomputational Life Science from MEXT.  ... 
doi:10.2197/ipsjtbio.5.27 fatcat:n2a5cp4sdzdvtb7fkzkeabnyde

Bioinformatics of alternative splicing and its regulation

Liliana Florea
2006 Briefings in Bioinformatics  
The sequencing of the human genome and ensuing wave of data generation have brought new light upon the extent and importance of alternative splicing as an RNA regulatory mechanism.  ...  Large EST data sets and sequence data from multiple genomes are fueling efforts to develop new computational methods to address these problems.  ...  Acknowledgment Thanks to Rosane Charlab for her careful review of the manuscript.  ... 
doi:10.1093/bib/bbk005 pmid:16761365 fatcat:m3y6dxczujblnasvypznhww72i

ASPIC: a novel method to predict the exon-intron structure of a gene that is optimally compatible to a set of transcript sequences

Paola Bonizzoni, Raffaella Rizzi, Graziano Pesole
2005 BMC Bioinformatics  
We propose a method, based on a novel multiple genome-EST alignment algorithm, for the detection of splice sites.  ...  To avoid limitations of splice sites prediction (mainly, over-predictions) due to independent single EST alignments to the genomic sequence our approach performs a multiple alignment of transcript data  ...  We thank Gianluca Delia Vedova for his helpful suggestions on the preliminary design of ASPIC software, David Horner and Giulio Pavesi for helpful comments on the manuscript and Gabriele Ravanelli for  ... 
doi:10.1186/1471-2105-6-244 pmid:16207377 pmcid:PMC1276783 fatcat:rmrmi5lj5zc7za4y6ynyd57j4u

Transcriptome Analysis for Non-Model Organism: Current Status and Best-Practices [chapter]

Vahap Eldem, Gokmen Zararsiz, Tunahan Taşçi, Izzet Parug Duru, Yakup Bakir, Melike Erkan
2017 Applications of RNA-Seq and Omics Strategies - From Microorganisms to Human Health  
Since transcriptome analysis provides genome-wide sequence and gene expression information, transcript reconstruction using RNA-Seq sequence reads has become popular during recent years.  ...  to coding or non-coding, but expressed, part of genome.  ...  Acknowledgements All authors contributed to the editing of the manuscript and the content is solely the responsibility of the authors.  ... 
doi:10.5772/intechopen.68983 fatcat:vatg4hbanrchxhuxbf3meb3hye

Widespread polycistronic transcripts in mushroom-forming fungi revealed by single-molecule long-read mRNA sequencing [article]

Sean Gordon, Elizabeth Tseng, Asaf Salamov, Jiwei Zhang, Xiandong Meng, Zhiying Zhao, Dongwan Don Kang, Jason Underwood, Igor V Grigoriev, Melania Figueroa, Jonathan S Schilling, Feng Chen (+1 others)
2014 bioRxiv   pre-print
We found genome-wide prevalence of polycistronic transcription in these Agaricomycetes, and it involves up to 8% of the transcribed genes.  ...  In summary, our study revealed, for the first time, the genome prevalence of polycistronic transcription in a subset of fungi.  ...  Genome-wide mapping of alternative splicing in Arabidopsis thaliana. Genome Res 20, 45-58 (2010). 23. Wang, E.T. et al. Alternative isoform regulation in human tissue transcriptomes.  ... 
doi:10.1101/012542 fatcat:eabvpwrxdzdq3na2sdylp3fieq

iMapSplice: Alleviating reference bias through personalized RNA-seq alignment

Xinan Liu, James N. MacLeod, Jinze Liu, Honghuang Lin
2018 PLoS ONE  
The algorithm makes use of personal genomic information and performs an unbiased alignment towards genome indices carrying both reference and alternative bases.  ...  Genomic variants in both coding and non-coding sequences can have functionally important and sometimes deleterious effects on exon splicing of gene transcripts.  ...  Discussion RNA-seq is a widely adopted technique used in transcriptome profiling for a wide range of applications including differential expression analyses, novel isoform prediction, genomic variants  ... 
doi:10.1371/journal.pone.0201554 pmid:30096157 pmcid:PMC6086400 fatcat:qpk7whyxufcldpgzaunysxqvgy

SuperTranscript: a data driven reference for analysis and visualisation of transcriptomes [article]

Nadia M Davidson, Anthony DK Hawkins, Alicia Oshlack
2016 bioRxiv   pre-print
In addition we used Lace to combine reference and assembled transcriptomes for chicken and recovered the sequence of hundreds of gaps in the reference genome.  ...  SuperTranscripts are a substitute for a reference genome, consisting of all the unique exonic sequence, in transcriptional order, such that each gene is represented by a single sequence.  ...  In one case, block positions are defined by forks or divergences in the splice graph ("Standard Blocks"), in the second case, blocks are defined dynamically using splice junctions detected in the reads  ... 
doi:10.1101/077750 fatcat:vftrycmdczfr3ghy653vf6edzy

Alternative splicing: Human disease and quantitative analysis from high-throughput sequencing

Wei Jiang, Liang Chen
2021 Computational and Structural Biotechnology Journal  
Alternative splicing contributes to the majority of protein diversity in higher eukaryotes by allowing one gene to generate multiple distinct protein isoforms.  ...  It adds another regulation layer of gene expression. Up to 95% of human multi-exon genes undergo alternative splicing to encode proteins with different functions.  ...  Acknowledgment This work has been supported by the National Institutes of Health [R01GM137428].  ... 
doi:10.1016/j.csbj.2020.12.009 pmid:33425250 pmcid:PMC7772363 fatcat:djkgvvsmrrdjxhowjkqheneypu
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