BACKGROUND: A number of completely sequenced eukaryotic genome data are available in the public domain. Eukaryotic genes are either 'intron containing' or 'intronless'. Eukaryotic 'intronless' genes are interesting datasets for comparative genomics and evolutionary studies. The SEGE database containing a collection of eukaryotic single exon genes is available. However, SEGE is derived using GenBank. The redundant, incomplete and heterogeneous qualities of GenBank data are a bottleneck for biological investigation in comparative genomics and evolutionary studies. Such studies often require representative gene sets from each genome and this is possible only by deriving specific datasets from completely sequenced genome data. Thus Genome SEGE, a database for 'intronless' genes in completely sequenced eukaryotic genomes, has been constructed. AVAILABILITY: http://sege.ntu.edu.sg/wester/intronless DESCRIPTION: Eukaryotic 'intronless' genes are extracted from nine completely sequenced genomes (four of which are unicellular and five of which are multi-cellular). The complete dataset is available for download. Data subsets are also available for 'intronless' pseudo-genes. The database provides information on the distribution of 'intronless' genes in different genomes together with their length distributions in each genome. Additionally, the search tool provides pre-computed PROSITE motifs for each sequence in the database with appropriate hyperlinks to InterPro. A search facility is also available through the web server. CONCLUSIONS: The unique features that distinguish Genome SEGE from SEGE is the service providing representative 'intronless' datasets for completely sequenced genomes. 'Intronless' gene sets available in this database will be of use for subsequent bio-computational analysis in comparative genomics and evolutionary studies. Such analysis may help to revisit the original genome data for re-examination and re-annotation.

SUMMARY: Binding of short antigenic peptides to Major histocompatibility complex (MHC) proteins is the first step in T-cell mediated immune response. To understand the structural principles governing MHC-specific peptide recognition and binding, we have developed the MHC-Peptide Interaction Database (MPID), containing sequence-structure-function information. MPID (version 1.2) contains curated x-ray crystallographic data on 86 MHC peptide complexes, with precomputed interaction parameters (solvent accessibility, hydrogen bonds, gap volume and gap index). A user-friendly web interface and query tools will facilitate the development of predictive algorithms for MHC-peptide binding from a structural viewpoint. AVAILABILITY: Freely accessible from http://surya.bic.nus.edu.sg/mpid.

UNLABELLED: Eukaryotes have both 'intron containing' and 'intron less' genes. Several databases are available for 'intron containing' genes in eukaryotes. In this note, we describe a database for 'intron less' genes from eukaryotes. 'Intron less' eukaryotic genes having prokaryotic architecture will help to understand gene evolution in a much simpler way unlike 'intron containing' genes. AVAILABILITY: SEGE is available at http://intron.bic.nus.edu.sg/seg/ CONTACT: [email protected]

Abstract Summary: IE-Kb (Intron Exon-Knowledge base) illustrates the intron–exon dynamics in eukaryotic genes. We have developed three different knowledge sets, namely ‘Non-redundant ExInt’, ‘Non-redundant Pfam-ExInt complement’ and ‘Non-redundant GenBank eukaryotic subdivisional sets’ to understand this phenomenon. Statistical analysis is performed on each knowledge set and the results are made available online. The entries in knowledge sets are ranked based on their intron length, exon length and protein length with relational hyper-links to the corresponding intron phase, intron position, intron sequence, gene definition and parent GenBank entry. Availability: http://intron.bic.nus.edu.sg/iekb/iekb.html Contact: [email protected] * To whom correspondence should be addressed.