EST-PAC a web package for EST annotation and protein sequence prediction

Source Code for Biology and Medicine

Volumn 1, Issue , 2006, Pages

  Strahm, Yvan ^a   Powell, David ^a   Lefèvre, Christophe ^a,b  

^a MONASH UNIVERSITY   (Australia)

^b UNIVERSITY OF MELBOURNE   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 34250811920     PISSN: None     EISSN: 17510473     Source Type: Journal    
DOI: 10.1186/1751-0473-1-2     Document Type: Article

References (22)

1. Adams MD Kelley JM Gocayne JD Dubnick M Polymeropoulos MH Xiao H Merril CR Wu A Olde B Moreno RF Complementary DNA sequencing: Expressed sequence tags and human genome project Science 1991 252 1651-1656 10.1126/science.2047873 2047873
2. Dias Neto E Correa RG Verjovski-Almeida S Briones MR Nagai MA da Silva W Zago MA Bordin S Costa FF Goldman GH Carvalho AF Matsukuma A Baia GS Simpson DH Brunstein A de Oliveira PS Bucher P Jongeneel CV O'Hare MJ Soares F Brentani RR Reis LF de Souza SJ Simpson AJ Shotgun sequencing of the human transcriptome with ORF expressed sequence tags Proc Natl Acad Sci USA 2000 97 3491-3496 16267 10737800 10.1073/pnas.97.7.3491
3. Hillier LD Lennon G Becker M Bonaldo MF Chiapelli B Chissoe S Dietrich N DuBuque T Favello A Gish W Hawkins M Hultman M Kucaba T Lacy M Le M Le N Mardis E Moore B Morris M Parsons J Prange C Rifkin L Rohlfing T Schellenberg K Marra M Generation and analysis of 280,000 human expressed sequence tags Genome Res 1996 6 807-828 8889549
4. Wistow G Bernstein SL Wyatt MK Fariss RN Behal A Touchman JW Bouffard G Smith D Peterson K Expressed sequence tag analysis of human RPE/choroid for the NEIBank Project: Over 6000 non-redundant transcripts, novel genes and splice variants Mol Vis 2002 8 205-220 12107410
5. Shivashankar HN Gasser RB Ranganathan S A hitchhiker's guide to expressed sequence tags (ESTs) and their bioinformatics analysis Briefings Bioinf
6. Bateman A Birney E Cerruti L Durbin R Etwiller L Eddy SR Griffiths-Jones S Howe KL Marshall M Sonnhammer EL The Pfam protein families database Nucleic Acids Res 2002 30 276-280 99071 11752314 10.1093/nar/30.1.276
7. Ayoubi P Jin X Leite S Liu X Martajaja J Abduraham A Wan Q Yan W Misawa E Prade RA PipeOnline 2.0: Automated EST processing and functional data sorting Nucleic Acids Res 2002 30 4761 4769 135791 12409467 10.1093/nar/ gkf585
8. Matukumalli LK Grefenstette JJ Sonstegard TS Van Tassell CP EST-PAGE. Managing and analyzing EST data Bioinformatics 2004 20 286 288 10.1093/ bioinformatics/btg411 14734326
9. Hotz-Wagenblatt A Hankeln T Ernst P Glatting KH Schmidt ER Suhai S ESTAnnotator: A tool for high throughput EST annotation Nucleic Acids Res 2003 31 3716-3719 169160 12824401 10.1093/nar/gkg566
10. Mao C Cushman JC May GD Weller JW ESTAP. An automated system for the analysis of EST data Bioinformatics 2003 19 1720-1722 10.1093/ bioinformatics/btg205 15593407
11. Parkinson J Anthony A Wasmuth J Schmid R Hedley A Blaxter M PartiGene. Constructing partial genomes Bioinformatics 2004 20 1398-1404 10.1093/ bioinformatics/bth101 14988115
12. Wasmuth JD Blaxter ML prot4EST: Translating expressed sequence tags from neglected genomes BMC Bioinformatics 2004 5 187 543579 15571632 10.1186/ 1471-2105-5-187
13. MySQL http://www.mysql.com
14. PHP http://www.php.net
15. McGinnis S Madden TL BLAST: At the core of a powerful and diverse set of sequence analysis tools Nucleic Acids Res 2004 32 W20-25 441573 15215342 10.1093/nar/gnh003
16. Iseli C Jongeneel CV Bucher P ESTScan: A program for detecting, evaluating, and reconstructing potential coding regions in EST sequences Proc Int Conf Intell Syst Mol Biol 1999 138-148 10786296
17. Lottaz C Iseli C Jongeneel CV Bucher P Modeling sequencing errors by combining Hidden Markov models Bioinformatics 2003 19 Suppl 2 103-112
18. Eddy SR Profile hidden Markov models Bioinformatics 1998 14 755-763 10.1093/bioinformatics/14.9.755 9918945
19. Pfam http://www.sanger.ac.uk/Software/Pfam
20. BioPerl http://bio.perl.org
21. NCBI BLAST http://www.ncbi.nlm.nih.gov/blast
22. EST-PAC http://vbc.med.monash.edu.au/~yvan/est-pac EST-PAC