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Literature DB >> 16600017

Reference based annotation with GeneMapper.

Abstract

We introduce GeneMapper, a program for transferring annotations from a well annotated genome to other genomes. Drawing on high quality curated annotations, GeneMapper enables rapid and accurate annotation of newly sequenced genomes and is suitable for both finished and draft genomes. GeneMapper uses a profile based approach for mapping genes into multiple species, improving upon the standard pairwise approach. GeneMapper is freely available for academic use.

Entities: Disease Gene Species

Mesh：

Year: 2006 PMID： 16600017 PMCID： PMC1557983 DOI： 10.1186/gb-2006-7-4-r29

Source DB: PubMed Journal: Genome Biol ISSN： 1474-7596 Impact factor: 13.583

30 in total

1. ECgene: genome-based EST clustering and gene modeling for alternative splicing.

Authors: Namshin Kim; Seokmin Shin; Sanghyuk Lee
Journal: Genome Res Date: 2005-04 Impact factor: 9.043

2. JIGSAW: integration of multiple sources of evidence for gene prediction.

Authors: Jonathan E Allen; Steven L Salzberg
Journal: Bioinformatics Date: 2005-08-02 Impact factor: 6.937

3. ExonHunter: a comprehensive approach to gene finding.

Authors: Brona Brejová; Daniel G Brown; Ming Li; Tomás Vinar
Journal: Bioinformatics Date: 2005-06 Impact factor: 6.937

4. Large multiple organism gene finding by collapsed Gibbs sampling.

Authors: Sourav Chatterji; Lior Pachter
Journal: J Comput Biol Date: 2005 Jul-Aug Impact factor: 1.479

5. Fast comparison of a DNA sequence with a protein sequence database.

Authors: X Huang
Journal: Microb Comp Genomics Date: 1996

6. A generalized hidden Markov model for the recognition of human genes in DNA.

Authors: D Kulp; D Haussler; M G Reese; F H Eeckman
Journal: Proc Int Conf Intell Syst Mol Biol Date: 1996

7. GMAP: a genomic mapping and alignment program for mRNA and EST sequences.

Authors: Thomas D Wu; Colin K Watanabe
Journal: Bioinformatics Date: 2005-02-22 Impact factor: 6.937

8. Gene recognition via spliced sequence alignment.

Authors: M S Gelfand; A A Mironov; P A Pevzner
Journal: Proc Natl Acad Sci U S A Date: 1996-08-20 Impact factor: 11.205

9. The Vertebrate Genome Annotation (Vega) database.

Authors: J L Ashurst; C-K Chen; J G R Gilbert; K Jekosch; S Keenan; P Meidl; S M Searle; J Stalker; R Storey; S Trevanion; L Wilming; T Hubbard
Journal: Nucleic Acids Res Date: 2005-01-01 Impact factor: 16.971

10. FlyBase: genes and gene models.

Authors: Rachel A Drysdale; Madeline A Crosby
Journal: Nucleic Acids Res Date: 2005-01-01 Impact factor: 16.971

26 in total

1. DNA-energetics-based analyses suggest additional genes in prokaryotes.

Authors: Garima Khandelwal; Jalaj Gupta; B Jayaram
Journal: J Biosci Date: 2012-07 Impact factor: 1.826

2. Patterns of gene duplication and intron loss in the ENCODE regions suggest a confounding factor.

Authors: Sourav Chatterji; Lior Pachter
Journal: Genomics Date: 2007-05-11 Impact factor: 5.736

3. A Functional Role for Antibodies in Tuberculosis.

Authors: Lenette L Lu; Amy W Chung; Tracy R Rosebrock; Musie Ghebremichael; Wen Han Yu; Patricia S Grace; Matthew K Schoen; Fikadu Tafesse; Constance Martin; Vivian Leung; Alison E Mahan; Magdalena Sips; Manu P Kumar; Jacquelynne Tedesco; Hannah Robinson; Elizabeth Tkachenko; Monia Draghi; Katherine J Freedberg; Hendrik Streeck; Todd J Suscovich; Douglas A Lauffenburger; Blanca I Restrepo; Cheryl Day; Sarah M Fortune; Galit Alter
Journal: Cell Date: 2016-09-22 Impact factor: 41.582

4. Population Structure of the Blue Swimmer Crab Portunus pelagicus in Coastal Areas of Malaysia Inferred from Microsatellites.

Authors: Chuan Jian Chai; Yuzine Bin Esa; Syukri Ismail; Mohd Salleh Kamarudin
Journal: Zool Stud Date: 2017-10-16 Impact factor: 2.058

5. Diverse molecular data demonstrate that commercially available medicinal leeches are not Hirudo medicinalis.

Authors: Mark E Siddall; Peter Trontelj; Serge Y Utevsky; Mary Nkamany; Kenneth S Macdonald
Journal: Proc Biol Sci Date: 2007-06-22 Impact factor: 5.349

6. Genomic Porosity between Invasive Chondrostoma nasus and Endangered Endemic Parachondrostoma toxostoma (Cyprinidae): The Evolution of MHC IIB Genes.

Authors: Andrea Simková; Kristína Civáňová; Lenka Gettová; André Gilles
Journal: PLoS One Date: 2013-06-18 Impact factor: 3.240

7. Revisiting the missing protein-coding gene catalog of the domestic dog.

Authors: Thomas Derrien; Julien Thézé; Amaury Vaysse; Catherine André; Elaine A Ostrander; Francis Galibert; Christophe Hitte
Journal: BMC Genomics Date: 2009-02-04 Impact factor: 3.969

8. Non-homogeneous combination of two porous genomes induces complex body shape trajectories in cyprinid hybrids.

Authors: Melthide Sinama; André Gilles; Caroline Costedoat; Emmanuel Corse; Jean-Michel Olivier; Rémi Chappaz; Nicolas Pech
Journal: Front Zool Date: 2013-05-01 Impact factor: 3.172

9. Ecological genetics of Chinese rhesus macaque in response to mountain building: all things are not equal.

Authors: Shan-Jin Wu; Jing Luo; Qing-Qing Li; Yan-Qin Wang; Robert W Murphy; Christopher Blair; Shi-Fang Wu; Bi-Song Yue; Ya-Ping Zhang
Journal: PLoS One Date: 2013-02-06 Impact factor: 3.240

10. Does invasive Chondrostoma nasus shift the parasite community structure of endemic Parachondrostoma toxostoma in sympatric zones?

Authors: Andrea Simková; Petra Navrátilová; Martina Dávidová; Markéta Ondračková; Melthide Sinama; Rémi Chappaz; André Gilles; Caroline Costedoat
Journal: Parasit Vectors Date: 2012-09-11 Impact factor: 3.876