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trome, trEST and trGEN: Databases of predicted protein sequences

Authors:
Peter Sperisen at Nestlé S.A.
Peter Sperisen
Christian Iseli at École Polytechnique Fédérale de Lausanne
Christian Iseli
Marco Pagni at Swiss Institute of Bioinformatics
Marco Pagni
Brian Stevenson at Swiss Institute of Bioinformatics
Brian Stevenson
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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.
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trome, trEST and trGEN: databases of predicted
protein sequences
Peter Sperisen
1
,
*, Christian Iseli
1
,
3
, Marco Pagni
1
,
3
, Brian J. Stevenson
1
,
3
,
Philipp Bucher
1
,
2
and C. Victor Jongeneel
1
,
3
1
Swiss Institute of Bioinformatics,
2
ISREC and
3
Of®ce of Information Technology, Ludwig Institute for Cancer
Research, Chemin des Boveresses 155, 1066 Epalinges s/Lausanne, Switzerland
Received September 15, 2003; Revised and Accepted September 29, 2003
ABSTRACT
We previously introduced two new protein data-
bases (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.
DESCRIPTION OF DATABASES
High-throughput genome (HTG) and expressed sequence tag
(EST) sequences are currently the most abundant nucleotide
sequence classes in the public databases. The large volume,
high degree of fragmentation and lack of gene structure
annotations prevent ef®cient searches of HTG and EST data
for protein sequence homologies by standard search methods.
We have compiled three databases of predicted and annotated
protein sequences to facilitate the use of proteomics tools. All
databases are distributed in a Swiss-Prot-like format, with
features that are speci®c to the databases presented below.
trome
trome is an attempt to map transcribed RNA from different
sources to the NCBI RefSeq genome sequence (1,2). As an
example, for Homo sapiens the transcribed RNA sources are:
the human EST section of the EMBL database (3), the human
HTC section of the EMBL database, human mRNA docu-
mented in the EMBL database, ORESTES sequences from
the LICR/FAPESP Human Cancer Genome project (4,5),
human mRNA documented in the NCBI-curated RefSeq
database [http://www.ncbi.nih.gov/RefSeq (6)], published
CHR21 gene list and SEREX sequences [http://www2.licr.
org/CancerImmunomeDB (7)]. For other species, similar
sources are used. Currently four species are represented:
H.sapiens, Mus musculus, Drosophila melanogaster,
Arabidopsis thaliana and Caenorhabditis elegans (Table 1).
The mapping of the transcribed RNA sources to the genome is
a three-step process (1,2):
(i) The program Megablast (8) is used to identify pairwise
similarities between all known transcript sequences and the
genomic data.
(ii) For each pair of matching RNA and genomic sequences,
local alignments were generated using a modi®ed version of
sim4 (9).
(iii) The output of sim4 was ®ltered to eliminate all
alignments that did not contain at least one region (exon)
matching with at least 95% identity over their high-quality
part and 88% over the remainder.
The output of sim4 is then used to generate directed acyclic
graphs using the program tromer (locally developed program
to automate the reconstruction of transcripts from transcript to
genome mapping). These graphs (the edges and nodes
represent exons/introns or splice donors/acceptors, respect-
ively) represent transcribed loci of the genome and contain in
a condensed form the information about all possible alterna-
tive splice variants that are experimentally documented. They
can be used to reconstruct virtual transcripts from the
underlying genomic sequence following a path from 3¢ tags
along experimentally veri®ed exon boundaries. Transcript
generation is a three-step process: (i) a seed edge is selected;
(ii) this edge is extended toward the 5¢ end and (iii) toward the
3¢ end. The seed edge is ®rst selected among unused 5¢-most
exons, then among any unused edge. The extension process
always attempts to include unused edges, which were derived
from the same RNA elements as the seed edge. The resulting
virtual transcripts are translated into protein sequences using
the program ESTScan (10). These protein sequences are the
basis of the trome database. ESTScan detects the coding frame
and corrects most frameshift errors introduced by sequencing
errors, but predicts their position within a range of a few amino
acids. Simulation experiments have shown that in 95% of the
cases the range is seven or fewer amino acids. To visualize this
uncertainty, the FT key UNSURE was used, indicating the
range within which the predicted sequence is more likely to
contain errors. However, due to the mapping of transcribed
RNA data onto the genome, this is a rare event in contrast to
*To whom correspondence should be addressed. Tel: +41 21 6925956; Fax: +41 21 6925945; Email: peter.sperisen@isb-sib.ch
Nucleic Acids Research, 2004, Vol. 32, Database issue D509±D511
DOI: 10.1093/nar/gkh067
Nucleic Acids Research, Vol. 32, Database issue ã Oxford University Press 2004; all rights reserved
corrections found in the database trEST (see below). The new
FT key EXON was introduced to indicate the positions of the
exon boundaries with respect to the NT contig.
FT EXON 1 173 Exon E0;NT_026943[46041..46562].
FT EXON 174 174 AA on splice site: tt/g -> L.
FT EXON 175 405 Exon E1;NT_026943[56062..56757].
FT EXON 406 406 AA on splice site: a/tg -> M.
FT EXON 407 514 Exon E2;NT_026943[63614..64087]
FT UNSURE 507 514 Frameshift error at pos.: 514;
base inserted:
trEST and trGEN
trEST is an attempt to produce contigs from clusters of ESTs
and to translate them into proteins (11). In the past 2 years the
following improvements have been introduced:
(i) Initially trEST was composed only of protein sequences
that were generated through the translation of contigs
produced from UniGene clusters (12) using ESTScan.
Protein sequences of coding ESTs that are not present in any
UniGene cluster were also introduced into trEST.
(ii) The species list has been increased (see Table 1).
(iii) Exactly as described for the trome database, the FT key
UNSURE was used to re¯ect the uncertainty range in
frameshift error correction by the program ESTScan plus the
correction of internal stop codons. The parameters used with
ESTScan are adapted to the error prone contigs produced from
UniGene clusters as well as the ESTs, since frameshift errors
as well as internal stop codons are found more frequently as
compared to the database trome.
trEST is cross-referenced to the UniGene database for the
entries that are based on UniGene clusters and to the EMBL
database for the ESTs that do not belong to UniGene clusters.
The amino acid sequences of the trGEN database are
predicted from genomic sequences from the NCBI database or
from HTG sequences from the EMBL database. The
sequences are searched for putative genes and their coding
regions using the program Genscan (13). The following
improvements were introduced:
(i) The species Rattus norvegicus was added.
(ii) The predictions for H.sapiens, M.musculus,
R.norvegicus and A.thaliana are now made on the basis of
the NCBI reference genome sequences (NT contigs).
(iii) The new FT Key GENSCAN was introduced. It
contains the predictions made by the program Genscan. These
are: FIRST EXON, INTERNAL EXON, LAST EXON and
SINGLE EXON together with their associated p-values (sum
over all parses containing exon) calculated by GENSCAN,
which serve as an indication about the degree of certainty that
should be ascribed to exons predicted by the program
FT GENSCAN 1 226 FIRST EXON; p-value: 0.159.
FT GENSCAN 227 262 INTERNAL EXON; p-value: 0.093.
FT GENSCAN 263 269 INTERNAL EXON; p-value: 0.065.
FT GENSCAN 270 320 LAST EXON; p-value: 0.074.
(iv) The ID is composed of either the EMBL or NCBI
accession number of the contig on which the protein was
predicted, plus a number (_#) that enumerates the proteins as
they are found on the contig.
(v) trGEN is cross-referenced to either the EMBL or the
NCBI RefSeq database, with a cross-link to the underlying
contig.
UPDATE TO THE DATABASES
The trEST and the trGEN databases are updated on a weekly
basis. The trome database is updated roughly every 3 months.
ACCESS
FTP
The ®les for the three databases are available by anonymous
ftp from the directories: ftp://ftp.isrec.isb-sib.ch/pub/
databases/trest, ftp://ftp.isrec.isb-sib.ch/pub/databases/trgen
and ftp://ftp.isrec.isb-sib.ch/pub/databases/trome. In addition
user manuals which provide more details about the format of
each database are found in the individual directories.
WWW
Several web pages offer services that include the trome, trEST
and trGEN databases. http://www.ch.embnet.org/software/
fetch.html allows one to retrieve individual entries of trome,
trEST and trGEN. http://www.ch.embnet.org/software/
aBLAST.html allows the three databases of hypothetical
proteins to be searched using BLAST.
ACKNOWLEDGEMENTS
This work was supported by a grant from the Swiss federal
of®ce for education and health (OFES): 01.0101 which is part
of the TEMBLOR project (QLRI-CT-2001-00015) of the
Quality of Life and Management of living Resources
Programme and by the Ludwig Institute for Cancer Research.
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Jongeneel,C.V. (2002) Long-range heterogeneity at the 3¢ ends of human
mRNAs. Genome Res., 12, 1068±1074.
Table 1. Number of entries in each database for each species represented
(established September 5, 2003)
trGEN trEST trome
Homo sapiens 196110 1709305 121072
Mus musculus 225759 1018677 95754
Rattus norvegicus 293151 274511 n.a.
Drosophila melanogaster 128071 28254 20717
Arabidopsis thaliana 31424 39924 n.a.
Oryza sativa 111723 57269 n.a.
Bos taurus n.a. 88378 n.a.
Danio rerio n.a. 125453 n.a.
Hordeum vulgare n.a. 79315 n.a.
Triticum aestivum n.a. 146462 n.a.
Xenopus laevis n.a. 116084 n.a.
Zea mays n.a. 121846 n.a.
Caenorhabditis elegans n.a. n.a. 25841
Total 986238 3805478 263384
Due to the limited amount of data, not all species are represented in all
databases. Missing data are indicated by `n.a.'.
D510 Nucleic Acids Research, 2004, Vol. 32, Database issue
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Article
  • Feb 1998
The EMBL Nucleotide Sequence Database is a comprehensive database of DNA and RNA sequences directly submitted from researchers and genome sequencing groups and collected from the scientific literature and patent applications. In collaboration with DDBJ and GenBank the database is produced, maintained and distributed at the European Bioinformatics Institute (EBI) and constitutes Europe's primary nucleotide sequence resource. Database releases are produced quarterly and are distributed on CD-ROM. EBI's network services allow access to the most up-to-date data collection via Internet and World Wide Web interface, providing database searching and sequence similarity facilities plus access to a large number of additional databases.
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Introducing RefSeq and LocusLink: Curated human genome resources at the NCBI
Article
  • Feb 2000
  • TRENDS GENET
RefSeq records are included in the Entrez retrieval system (http://www.ncbi.nlm.nih.gov/entrez/). This allows a third query pathway, namely directly by Entrez nucleotide or protein text queries or indirectly by neighboring strategies. LocusLink and RefSeq data are also provided without restriction for ftp transfer (ftp://ncbi.nlm.nih.gov/refseq). Therefore, the combination of LocusLink and RefSeq resources provides a powerful approach to answering such questions as: •Is my sequence from a known gene? (Try blast and look for a RefSeq result.)•What sequence can I use as a standard for gene A? (Try blast or LocusLink.)•Where can I get more information about gene B? (Start at LocusLink.)•What genes are related to disorder Z? (Start at OMIM or LocusLink.)The goal of LocusLink and RefSeq is to include all known genes and their major products. As of the end of August 1999, ∼10 690 loci have been included, 7500 with at least some sequence data and 5985 reference mRNAs. Expanding the LocusLink and RefSeq datasets is an ongoing effort – LocusIDs are established as additional genes are identified, and RefSeq records are added as new links between genes and sequences with complete coding regions are made. The public sites are refreshed weekly. We welcome collaborations with the scientific community to ensure that these resources are as comprehensive and accurate as possible.
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