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A graph based algorithm for generating EST consensus sequences

K. Malde, E. Coward, I. Jonassen
2004 Bioinformatics  
Results: In contrast to the more established assembly tools, we propose an algorithm that constructs a graph over sequence fragments of fixed size, and produces consensus sequences as traversals of this  ...  Motivation: EST sequences constitute an abundant, yet error prone resource for computational biology.  ...  CAP3 is freely available for academic use, and was provided pre-compiled, along with advice on using it for EST clustering, by its author, Xiaoqiu Hang (pers. comm.).  ... 
doi:10.1093/bioinformatics/bti184 pmid:15572463 fatcat:f5hywccirfg25inzitwgm5ntga

Generating consensus sequences from partial order multiple sequence alignment graphs

C. Lee
2003 Bioinformatics  
Here we present a dynamic programming algorithm (heaviest bundle) for generating multiple consensus sequences from such complex alignments.  ...  Motivation: Consensus sequence generation is important in many kinds of sequence analysis ranging from sequence assembly to profile-based iterative search methods.  ...  Xing for their helpful discussions and comments on this work.  ... 
doi:10.1093/bioinformatics/btg109 pmid:12761063 fatcat:vme7737mtfbnpgkifyclxc6twa

Splicing graphs and EST assembly problem

Steffen Heber, Max Alekseyev, Sing-Hoi Sze, Haixu Tang, Pavel A. Pevzner
2002 Computer applications in the biosciences : CABIOS  
We further design an algorithm to assemble EST reads into the splicing graph rather than assembling them into each splicing variant in a case-by-case fashion. Availability:  ...  a path in the graph.  ...  ACKNOWLEDGMENTS The authors are grateful to Tim Beißbarth, Eivind Coward, Stefan Haas, Antje Krause, Christopher Lee, and Zufar Mulyukov for help and very valuable discussions.  ... 
doi:10.1093/bioinformatics/18.suppl_1.s181 pmid:12169546 fatcat:xvbsisisyraarjwzyrj3zcmwoy

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

Y. Xing
2004 Genome Research  
We analyze this "multiassembly problem"-reconstructing the most likely set of full-length isoform sequences from a mixture of EST fragment data-and present a graph-based algorithm for solving it.  ...  One challenge is the fact that most high-throughput experimental methods for characterizing transcripts (such as EST sequencing) give highly detailed information about short fragments of transcripts or  ...  One central resource has been the construction of a consensus sequence for each group of ESTs (Quackenbush et al. 2000) .  ... 
doi:10.1101/gr.1304504 pmid:14962984 pmcid:PMC353230 fatcat:ujgmvlcrmzcyfaq7xhrwbddshe

Mining Plutella xylostella's expressed sequence tags (EST) for a functionally annotated candidate gene index

Dinakar R. Ampasala, M. Pritika, Mohane Selvaraj Coumar, Amouda Venkatsan
2016 Indian Journal of Agricultural Research  
Expressed Sequence Tags (ESTs, 37,915) of the insect obtained from GenBank were clustered and consensus sequences (4224) were constructed using mining tool (CAP3).  ...  One of the mapped candidate gene codes for aldehyde dehydrogenase enzyme, which is potentially involved in xenobiotic detoxification of synthetic insecticides, and play a role in the development of resistance  ...  In the DAGs generated for molecular function (Figure 2 Based on the number of sequences at each node of DAG, a cut off value of five per node was assigned to generate overall consensus sequence annotation  ... 
doi:10.18805/ijare.v50i1.8584 fatcat:r4pvsqaxifadvdx3advni3j2lq

Getting insight into the pan-genome structure with PangTree

Paulina Dziadkiewicz, Norbert Dojer
2020 BMC Genomics  
This work focuses on providing a tool for discovering and visualizing the relationships between the sequences constituting a pan-genome.  ...  Each node of this tree has assigned a subset of genomes, as well as their homogeneity level and averaged consensus sequence.  ...  Acknowledgements We thank Anna Lisiecka for implementing the Mafgraph tool. About this supplement  ... 
doi:10.1186/s12864-020-6610-4 pmid:32299360 pmcid:PMC7161101 fatcat:rjutjgz7gzex7h6ui5r2evvq7i

A consistency-based consensus algorithm for de novo and reference-guided sequence assembly of short reads

T. Rausch, S. Koren, G. Denisov, D. Weese, A.-K. Emde, A. Doring, K. Reinert
2009 Bioinformatics  
A robust and versatile consensus tool is of particular interest for such data since a sound multi-read alignment is a prerequisite for variation analyses, accurate genome assemblies and insert sequencing  ...  Results: A multi-read alignment algorithm for de novo or referenceguided genome assembly is presented.  ...  ACKNOWLEDGEMENTS We wish to thank the AMOS group at the CBCB at the University of Maryland for valuable input on the use of the AMOS library.  ... 
doi:10.1093/bioinformatics/btp131 pmid:19269990 pmcid:PMC2732307 fatcat:h5spu6a4dfgwlfesroaogogubi

Computational methods for alternative splicing prediction

P. Bonizzoni
2006 Briefings in Functional Genomics & Proteomics  
Here, we provide an overview of current methods for the computational prediction of alternative splicing based on the alignment of genome and transcript sequences.  ...  The fact that a large majority of mammalian genes are subject to alternative splicing indicates that this phenomenon represents a major mechanism for increasing proteome complexity.  ...  The authors thank David Horner for his helpful comments on the manuscript.  ... 
doi:10.1093/bfgp/ell011 pmid:16769678 fatcat:agpf2erqgbfnpmzfftlvs4svim

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  
Our method, which relies both on the Partial Order Alignment (POA) program for constructing multiple sequence alignments, and its Heaviest Bundling function for generating consensus sequences, accounts  ...  We present a method for high-throughput alternative splicing detection in expressed sequence data.  ...  Remarkably, a single consensus sequence was generated for only 16% of the Human UniGene clusters; two or three consensus sequences were generated for 41% of the clusters; four to ten consensus sequences  ... 
doi:10.1142/9789812704856_0004 fatcat:pnniwrkgmbenpf5efdefv5lmdy

RCDA: A highly sensitive and specific alternatively spliced transcript assembly tool featuring upstream consecutive exon structures

Xiaolu H. Sturgeon, Katheleen J. Gardiner
2012 Genomics  
Here, we describe RCDA, a genome-based transcript assembly tool comprising RCluster, that recursively clusters transcripts, and DAssemble, that generates composite transcript sequences through path-finding  ...  using a directed acyclic graph.  ...  Acknowledgments This work was supported by the Fondation Jerome Lejeune, the Coleman Institute for Cognitive Deficits, the Linda Crnic Institute for Down Syndrome and the National Institutes of Health  ... 
doi:10.1016/j.ygeno.2012.08.004 pmid:22971325 pmcid:PMC5470730 fatcat:zuphim46zjbzngsugt47ckc7ay

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

B. Modrek
2001 Nucleic Acids Research  
Our method, which relies both on the Partial Order Alignment (POA) program for constructing multiple sequence alignments, and its Heaviest Bundling function for generating consensus sequences, accounts  ...  We present a method for high-throughput alternative splicing detection in expressed sequence data.  ...  Remarkably, a single consensus sequence was generated for only 16% of the Human UniGene clusters; two or three consensus sequences were generated for 41% of the clusters; four to ten consensus sequences  ... 
doi:10.1093/nar/29.13.2850 pmid:11433032 pmcid:PMC55780 fatcat:xlmy2izienhczbvlxv7absqmdy

De Novo Repeat Classification and Fragment Assembly

P. A. Pevzner
2004 Genome Research  
y x x Consistent Gluing Challenge: Generalize the Notion of De Bruijn Graph for Imperfect Repeats • Input -a genomic sequence -all significant local pairwise alignments • Output -repeat  ...  8 9 10 11 12 13 14 15 y y x x repeat graph Minimum (or Maximum) Spanning Trees • The first algorithm for finding a MST was developed by Boruvka in 1926 to minimize the cost of electrical  ...  into a single sequence • Compute the similarity matrix for this concatenated sequence (overlap detection between reads) • Use this matrix as a "glue" to build the repeat graph with the RepeatGluer algorithm  ... 
doi:10.1101/gr.2395204 pmid:15342561 pmcid:PMC515325 fatcat:rtjukazb5zeglbc356rhmvpm2y

ECgene: Genome-based EST clustering and gene modeling for alternative splicing

N. Kim
2005 Genome Research  
With the availability of the human genome map and fast algorithms for sequence alignment, genome-based EST clustering became a viable method for gene modeling.  ...  Sequences that share any splice sites are grouped together to define an EST cluster in a manner similar to that of the genome-based version of the UniGene algorithm.  ...  Acknowledgments We thank the UCSC Genome Center for making such a wonderful resource available to the public. We would also like to thank Prof.  ... 
doi:10.1101/gr.3030405 pmid:15805497 pmcid:PMC1074371 fatcat:yhmzjpewjree7ee3zgpx4dyh3e

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  
For non-model organism, as distinct from the reference genome-based mapping, sequence reads are processed via de novo transcriptome assembly approaches to produce large numbers of contigs corresponding  ...  to be taken in a step-by-step manner.  ...  This work was partly supported by the Istanbul University Scientific Research Project (Project No. 46473 and 29506) and also partly supported by Marmara University Research Fund (Grant Number: FEN-A-100616  ... 
doi:10.5772/intechopen.68983 fatcat:vatg4hbanrchxhuxbf3meb3hye

De Novo Transcriptome Assembly Of Solid Sequencing Data In Cucumis Melo

Purru Supriya
2015 Zenodo  
In the present study, we have carried out a comparison of two assemblers (SeqMan and CLC) for transcriptome assembly, using a new dataset from Cucumis melo.  ...  Combining the assemblies from different programs gave a more credible final product, and therefore this approach is recommended for quantitative output.  ...  In the third phase, a multiple sequence alignment of reads is constructed and a consensus sequence along with a quality value for each base is computed for each contig.  ... 
doi:10.5281/zenodo.1309156 fatcat:ql3ta3n4szh4na4zk6ma5vyaa4
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