FIE2: A program for the extraction of genomic DNA sequences around the start and translation initiation site of human genes

Nucleic Acids Research

Volumn 31, Issue 13, 2003, Pages 3546-3553

  Chong, Allen ^a   Zhang, Guanglan ^a   Bajic, Vladimir B ^a  

^a INSTITUTE FOR INFOCOMM RESEARCH   (Singapore)

Author keywords

[No Author keywords available]

Indexed keywords

GENOMIC DNA; MESSENGER RNA;

5' UNTRANSLATED REGION; ACCESS TO INFORMATION; ACCURACY; ARTICLE; CHROMOSOME; COMPUTER PROGRAM; DNA SEQUENCE; HUMAN; INFORMATION PROCESSING; INTERNET; LOCUSLINK; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROMOTER REGION; SEQUENCE ANALYSIS; SEQUENCE DATABASE; TRANSLATION INITIATION; CHEMISTRY; EVALUATION; GENOME; METHODOLOGY; MOLECULAR GENETICS; RNA TRANSLATION; SEQUENCE ALIGNMENT; TRANSCRIPTION INITIATION SITE;

BASE SEQUENCE; GENOME, HUMAN; HUMANS; INTERNET; MOLECULAR SEQUENCE DATA; PEPTIDE CHAIN INITIATION, TRANSLATIONAL; PROMOTER REGIONS (GENETICS); RNA, MESSENGER; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; SEQUENCE ANALYSIS, RNA; SOFTWARE; TRANSCRIPTION INITIATION SITE;

EID: 0042121199     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkg604     Document Type: Article

References (25)

1. Maglott,D.R., Katz,K.S., Sicotte,H. and Pruitt,K.D. (2000) NCBI's LocusLink and RefSeq. Nucleic Acids Res., 28, 126-128.
2. Pruitt,K.D., Katz,K.S., Sicotte,H. and Maglott,D.R. (2000) Introducing RefSeq and LocusLink: curated human genome resources at the NCBI. Trends Genet., 16, 44-47.
3. Pruitt,K.D. and Maglott,D.R. (2000) RefSeq and LocusLink: NCBI gene-centered resources. Nucleic Acids Res., 29, 137-140.
4. Zhang,T and Zhang,M. (2001) Promoter Extraction from GenBank (PEG): automatic extraction of eukaryotic promoter sequences in large sets of genes. Bioinformatics, 17, 1232-1233.
5. Zhang,H., Ramanathan,Y., Soteropoulos,P., Recce,M.L. and Tolias,P.P. (2002) EZ-Retrieve: a web-server for batch retrieval of coordinate-spccified human DNA sequences and underscoring putative transcription factor binding sites. Nucleic Acids Res., 30, e121.
6. Bajic,V.B., Chong,A., Seah,S.H. and Brusic,V. (2002) Intelligent system for vertebrate promoter recognition. IEEE Intelligent Systems, 17, 64-70.
7. Bajic,V.B., Seah,S.H., Chong,A., Zhang,G., Koh,J.L. and Brusic,V. (2002) Dragon Promoter Finder: recognition of vertebrate RNA polymerase II promoters. Bioinformatics, 18, 198-199.
8. Collins,J.E., Goward,M.E., Cole,C.G., Smink,L.J., Huckle,E.J., Knowles,S., Bye,J.M., Beare,D.M. and Dunham,I. (2003) Reevaluating human gene annotation: a second-generation analysis of chromosome 22. Genome Res., 13, 27-36.
9. Chong,A., Zhang,G. and Bajic,V.B. (2002) Information and sequence extraction around the 5′-end and translation initiation site of human genes. In Silico Biol., 2, 461-465.
10. Suzuki,Y., Yamashita,R., Nakai,K. and Sugano,S. (2002) DBTSS: DataBase of human Transcriptional Start Sites and full-length cDNAs. Nucleic Acids Res., 30, 329-331.
11. Yamashita,R., Suzuki,Y., Sugano,S. and Nakai,K. (2001) DBTSS: DataBase of Human Transcriptional Start Sites and Full-Length cDNA. Genome Informatics, 12, 488-489.
12. Suzuki,Y., Yoshitomo-Nakagawa,K., Maruyama,K., Suyama,A. and Sugano,S. (1997) Construction and characterization of a full length-enriched and a 5′-end-enriched cDNA library. Gene, 200, 149-156.
13. Maruyama,K. and Sugano,S. (1994) Oligo-capping: a simple method to replace the cap structure of eukaryotic mRNAs with oligoribonucleotides. Gene, 138, 171-174.
14. Nagase,T., Nakayama,M., Nakajima,D., Kikuno,R. and Ohara,O. (2001) Prediction of the coding sequences of unidentified human genes. XX. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro. DNA Res., 8, 85-95.
15. Ohara,O., Nagase,T., Ishikawa,K., Nakajima,D., Ohira,M., Seki,N. and Nomura,N. (1997) Construction and characterization of human brain cDNA libraries suitable for analysis of cDNA clones encoding relatively large proteins. DNA Res., 4, 53-59.
16. Wellenreuther,R., Wiemann,S., Heiss,D. and Poustka,A. (2001) Generating and sequencing full-length cDNAs of novel human genes within the German cDNA consortium. In 11th Annual Workshop: Beyond the Identification of Transcribed Sequences: Functional and Expression Analysis, Washington DC.
17. Wiemann,S., Weil,B., Wellenreuther,R., Gassenhuber,J., Glassl,S., Ansorge,W., Bocher,M., Blocker,H., Bauersachs,S., Blum,H. et al. (2001) Toward a catalog of human genes and proteins: sequencing and analysis of 500 novel complete protein coding human cDNAs. Genome Res., 11, 422-435.
18. Lennon,G., Auffray,C., Polymeropoulos,M. and Soares,M.B. (1996) The I.M.A.G.E. Consortium: an integrated molecular analysis of genomes and their expression. Genomics, 33, 151-152.
19. Shah,N.P., Witte,O.N. and Denny,C.T. (1991) Characterization of the BCR promoter in Philadelphia chromosome-positive and -negative cell lines. Mol. Cell. Biol., 11, 1854-1860.
20. Praz,V., Perier,R., Bonnard,C. and Bucher,P. (2002) The Eukaryotic Promoter Database, EPD: new entry types and links to gene expression data. Nucleic Acids Res., 30, 322-324.
21. Perier,R.C., Praz,V., Junier,T., Bonnard,C. and Bucher,P. (2000) The eukaryotic promoter database (EPD). Nucleic Acids Res., 28, 302-303.
22. Wheeler,D.L., Church,D.M., Lash,A.E., Leipe,D.D., Madden,T.L., Pontius,J.U., Schuler,G.D., Schriml,L.M., Tatusova,T.A., Wagner,L. and Rapp,B.A. (2002) Database resources of the National Center for Biotechnology Information: 2002 update. Nucleic Acids Res., 30, 13-16.
23. Hubbard,T., Barker,D., Birney,E., Cameron,G., Chen,Y., Clark,L., Cox,T., Cuff,J., Curwen,V., Down,T. et al. (2002) The Ensembl genome database project. Nucleic Acids Res., 30, 38-41.
24. Kent,W.J., Sugnet,C.W., Furey,T.S., Roskin,K.M., Pringle,T.H., Zahler,A.M. and Haussler,D. (2002) The human genome browser at UCSC. Genome Res., 12, 996-1006.
25. Coleman,S.L., Buckland,P.R., Hoogendoom,B., Guy,C., Smith,K. and O'Donovan,M.C. (2002) Experimental analysis of the annotation of promoters in the public database. Hum. Mol. Genet., 11, 1817-1821.