Literature DB >> 15037510

BLAST2GENE: a comprehensive conversion of BLAST output into independent genes and gene fragments.

Mikita Suyama1, David Torrents, Peer Bork.   

Abstract

SUMMARY: BLAST2GENE is a program that allows a detailed analysis of genomic regions containing completely or partially duplicated genes. From a BLAST (or BL2SEQ) comparison of a protein or nucleotide query sequence with any genomic region of interest, BLAST2GENE processes all high scoring pairwise alignments (HSPs) and provides the disposition of all independent copies along the genomic fragment. The results are provided in text and PostScript formats to allow an automatic and visual evaluation of the respective region. AVAILABILITY: The program is available upon request from the authors. A web server of BLAST2GENE is maintained at http://www.bork.embl.de/blast2gene

Entities:  

Mesh：

Year:  2004        PMID： 15037510     DOI： 10.1093/bioinformatics/bth172

Source DB:  PubMed          Journal:  Bioinformatics        ISSN： 1367-4803            Impact factor:   6.937


  12 in total

1.  Complex genomic rearrangements lead to novel primate gene function.

Authors:  Francesca D Ciccarelli; Christian von Mering; Mikita Suyama; Eoghan D Harrington; Elisa Izaurralde; Peer Bork
Journal:  Genome Res       Date:  2005-02-14       Impact factor: 9.043

2.  GenBlastA: enabling BLAST to identify homologous gene sequences.

Authors:  Rong She; Jeffrey S-C Chu; Ke Wang; Jian Pei; Nansheng Chen
Journal:  Genome Res       Date:  2008-10-06       Impact factor: 9.043

3.  Computational Methods for Pseudogene Annotation Based on Sequence Homology.

Authors:  Paul M Harrison
Journal:  Methods Mol Biol       Date:  2021

4.  RNA-Seq improves annotation of protein-coding genes in the cucumber genome.

Authors:  Zhen Li; Zhonghua Zhang; Pengcheng Yan; Sanwen Huang; Zhangjun Fei; Kui Lin
Journal:  BMC Genomics       Date:  2011-11-02       Impact factor: 3.969

5.  Deep-coverage rhesus red blood cell proteome: a first comparison with the human and mouse red blood cell.

Authors:  Erica M Pasini; Morten Kirkegaard; Peter Mortensen; Matthias Mann; Alan W Thomas
Journal:  Blood Transfus       Date:  2010-06       Impact factor: 3.443

6.  Identification and analysis of genes and pseudogenes within duplicated regions in the human and mouse genomes.

Authors:  Mikita Suyama; Eoghan Harrington; Peer Bork; David Torrents
Journal:  PLoS Comput Biol       Date:  2006-05-16       Impact factor: 4.475

7.  PLOTREP: a web tool for defragmentation and visual analysis of dispersed genomic repeats.

Authors:  Gábor Tóth; Gábor Deák; Endre Barta; György B Kiss
Journal:  Nucleic Acids Res       Date:  2006-07-01       Impact factor: 16.971

8.  BOV--a web-based BLAST output visualization tool.

Authors:  Rajesh Gollapudi; Kashi Vishwanath Revanna; Chris Hemmerich; Sarah Schaack; Qunfeng Dong
Journal:  BMC Genomics       Date:  2008-09-15       Impact factor: 3.969

9.  Family expansion and gene rearrangements contributed to the functional specialization of PRDM genes in vertebrates.

Authors:  Irene Fumasoni; Natalia Meani; Davide Rambaldi; Gaia Scafetta; Myriam Alcalay; Francesca D Ciccarelli
Journal:  BMC Evol Biol       Date:  2007-10-04       Impact factor: 3.260

10.  BLASTGrabber: a bioinformatic tool for visualization, analysis and sequence selection of massive BLAST data.

Authors:  Ralf Stefan Neumann; Surendra Kumar; Thomas Hendricus Augustus Haverkamp; Kamran Shalchian-Tabrizi
Journal:  BMC Bioinformatics       Date:  2014-05-05       Impact factor: 3.169
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