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Literature DB >> 12824360

MGAlignIt: A web service for the alignment of mRNA/EST and genomic sequences.

Bernett T K Lee¹, Tin Wee Tan, Shoba Ranganathan.

Abstract

Splicing is a biological phenomenon that removes the non-coding sequence from the transcripts to produce a mature transcript suitable for translation. To study this phenomenon, information on the intron-exon arrangement of a gene is essential, usually obtained by aligning mRNA/EST sequences to their cognate genomic sequences. MGAlign is a novel, rapid, memory efficient and practical method for aligning mRNA/EST and genome sequences. We present here a freely available web service, MGAlignIt (http://origin.bic.nus.edu.sg/mgalign/mgalignit), based on MGAlign. Besides the alignment itself, this web service allows users to effectively visualize the alignment in a graphical manner and to perform limited analysis on the alignment output. The server also permits the alignment to be saved in several forms, both graphical and text, suitable for further processing and analysis by other programs.

Mesh：

Substances：
RNA, Messenger

Year: 2003 PMID： 12824360 PMCID： PMC168968 DOI： 10.1093/nar/gkg561

Source DB: PubMed Journal: Nucleic Acids Res ISSN： 0305-1048 Impact factor: 16.971

19 in total

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Journal: Trends Genet Date: 2001-02 Impact factor: 11.639

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Journal: Nature Date: 2001-02-15 Impact factor: 49.962

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Journal: Cell Date: 2000-10-27 Impact factor: 41.582

4. The PROSITE database, its status in 2002.

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Review 5. Alternative pre-mRNA splicing and proteome expansion in metazoans.

Authors: Tom Maniatis; Bosiljka Tasic
Journal: Nature Date: 2002-07-11 Impact factor: 49.962

6. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana.

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Journal: Hum Mol Genet Date: 2002-02-15 Impact factor: 6.150

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Journal: Nature Date: 2002-02-21 Impact factor: 49.962

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Journal: Science Date: 2001-02-16 Impact factor: 47.728

11 in total

1. e2g: an interactive web-based server for efficiently mapping large EST and cDNA sets to genomic sequences.

Authors: Jan Krüger; Alexander Sczyrba; Stefan Kurtz; Robert Giegerich
Journal: Nucleic Acids Res Date: 2004-07-01 Impact factor: 16.971

2. ASmodeler: gene modeling of alternative splicing from genomic alignment of mRNA, EST and protein sequences.

Authors: Namshin Kim; Seokmin Shin; Sanghyuk Lee
Journal: Nucleic Acids Res Date: 2004-07-01 Impact factor: 16.971

3. Functional characterization and localization of Pneumocystis carinii lanosterol synthase.

Authors: Tiffany M Joffrion; Margaret S Collins; Thomas Sesterhenn; Melanie T Cushion
Journal: Eukaryot Cell Date: 2009-11-06

4. Contrasting evolution of diversity at two disease-associated chicken genes.

Authors: Tim Downing; David J Lynn; Sarah Connell; Andrew T Lloyd; A K Fazlul Haque Bhuiyan; Pradeepa Silva; Arifa N Naqvi; Rahamame Sanfo; Racine-Samba Sow; Baitsi Podisi; Cliona O'Farrelly; Olivier Hanotte; Daniel G Bradley
Journal: Immunogenetics Date: 2009-02-27 Impact factor: 2.846

5. Protein encoding genes in an ancient plant: analysis of codon usage, retained genes and splice sites in a moss, Physcomitrella patens.

Authors: Stefan A Rensing; Dana Fritzowsky; Daniel Lang; Ralf Reski
Journal: BMC Genomics Date: 2005-03-22 Impact factor: 3.969

6. Molecular Characterization of Voltage-Gated Sodium Channels and Their Relations with Paralytic Shellfish Toxin Bioaccumulation in the Pacific Oyster Crassostrea gigas.

Authors: Floriane Boullot; Justine Castrec; Adeline Bidault; Natanael Dantas; Laura Payton; Mickael Perrigault; Damien Tran; Zouher Amzil; Pierre Boudry; Philippe Soudant; Hélène Hégaret; Caroline Fabioux
Journal: Mar Drugs Date: 2017-01-19 Impact factor: 5.118