pubmed.ncbi.nlm.nih.gov

trome, trEST and trGEN: databases of predicted protein sequences - PubMed

️Thu Jan 01 2004

trome, trEST and trGEN: databases of predicted protein sequences

Peter Sperisen et al. Nucleic Acids Res. 2004.

Abstract

We previously introduced two new protein databases (trEST and trGEN) of hypothetical protein sequences predicted from EST and HTG sequences, respectively. Here, we present the updates made on these two databases plus a new database (trome), which uses alignments of EST data to HTG or full genomes to generate virtual transcripts and coding sequences. This new database is of higher quality and since it contains the information in a much denser format it is of much smaller size. These new databases are in a Swiss-Prot-like format and are updated on a weekly basis (trEST and trGEN) or every 3 months (trome). They can be downloaded by anonymous ftp from ftp://ftp.isrec.isb-sib.ch/pub/databases.

PubMed Disclaimer

Cited by

MyHits: a new interactive resource for protein annotation and domain identification.
Pagni M, Ioannidis V, Cerutti L, Zahn-Zabal M, Jongeneel CV, Falquet L. Pagni M, et al. Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W332-5. doi: 10.1093/nar/gkh479. Nucleic Acids Res. 2004. PMID: 15215405 Free PMC article.
Revealing Missing Human Protein Isoforms Based on Ab Initio Prediction, RNA-seq and Proteomics.
Hu Z, Scott HS, Qin G, Zheng G, Chu X, Xie L, Adelson DL, Oftedal BE, Venugopal P, Babic M, Hahn CN, Zhang B, Wang X, Li N, Wei C. Hu Z, et al. Sci Rep. 2015 Jul 9;5:10940. doi: 10.1038/srep10940. Sci Rep. 2015. PMID: 26156868 Free PMC article.
An atlas of human gene expression from massively parallel signature sequencing (MPSS).
Jongeneel CV, Delorenzi M, Iseli C, Zhou D, Haudenschild CD, Khrebtukova I, Kuznetsov D, Stevenson BJ, Strausberg RL, Simpson AJ, Vasicek TJ. Jongeneel CV, et al. Genome Res. 2005 Jul;15(7):1007-14. doi: 10.1101/gr.4041005. Genome Res. 2005. PMID: 15998913 Free PMC article.
MyHits: improvements to an interactive resource for analyzing protein sequences.
Pagni M, Ioannidis V, Cerutti L, Zahn-Zabal M, Jongeneel CV, Hau J, Martin O, Kuznetsov D, Falquet L. Pagni M, et al. Nucleic Acids Res. 2007 Jul;35(Web Server issue):W433-7. doi: 10.1093/nar/gkm352. Epub 2007 Jun 1. Nucleic Acids Res. 2007. PMID: 17545200 Free PMC article.
The Protein Identifier Cross-Referencing (PICR) service: reconciling protein identifiers across multiple source databases.
Côté RG, Jones P, Martens L, Kerrien S, Reisinger F, Lin Q, Leinonen R, Apweiler R, Hermjakob H. Côté RG, et al. BMC Bioinformatics. 2007 Oct 18;8:401. doi: 10.1186/1471-2105-8-401. BMC Bioinformatics. 2007. PMID: 17945017 Free PMC article.

References

1. Iseli C., Stevenson,B.J., de Souza,S.J., Samaia,H.B., Camargo,A.A., Buetow,K.H., Strausberg,R.L., Simpson,A.J., Bucher,P. and Jongeneel,C.V. (2002) Long-range heterogeneity at the 3′ ends of human mRNAs. Genome Res., 12, 1068–1074. - PMC - PubMed
1. Stevenson B.J., Iseli,C., Beutler,B. and Jongeneel,C.V. (2003) Use of transcriptome data to unravel the fine structure of genes involved in sepsis. J. Infect. Dis., 187 (Suppl. 2), S308–S314. - PubMed
1. Stoesser G., Sterk,P., Tuli,M.A., Stoehr,P.J. and Cameron,G.N. (1997) The EMBL Nucleotide Sequence Database. Nucleic Acids Res., 25, 7–14. - PMC - PubMed
1. Dias N.E., Correa,R.G., Verjovski-Almeida,S., Briones,M.R., Nagai,M.A., da Silva,,W.,Jr, Zago,M.A., Bordin,S., Costa,F.F., Goldman,G.H. et al. (2000) Shotgun sequencing of the human transcriptome with ORF expressed sequence tags. Proc. Natl Acad. Sci. USA, 97, 3491–3496. - PMC - PubMed
1. Camargo A.A., Samaia,H.P., Dias-Neto,E., Simao,D.F., Migotto,I.A., Briones,M.R., Costa,F.F., Nagai,M.A., Verjovski-Almeida,S., Zago,M.A. et al. (2001) The contribution of 700 000 ORF sequence tags to the definition of the human transcriptome. Proc. Natl Acad. Sci. USA, 98, 12103–12108. - PMC - PubMed

trome, trEST and trGEN: databases of predicted protein sequences - PubMed