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GISSD

http://www.rna.whu.edu.cn/gissd

Description :
Group I Intron Sequence and Structure Database

ASTD

http://www.ebi.ac.uk/astd/

Description :
The Alternative Splicing Database (ASD) Project aims to understand the mechanism of alternative splicing on a genome-wide scale by creating a database of alternative splice events and the resultant isoform splice patterns of genes from human, and other model species.

At the moment three databases are available: AltSplice, AltExtron, and AEdb. AltSplice and AltExtron implement a computational pipeline that detects and characterise alternative intron/exons, alternative splice events, and isoform splice patterns. AltExtron considers gene entries from the EMBL database, while AltSplice considers gene entries from EnsEMBL. AEdb is the manually collected & curated (from literature) equivalent. AEdb comes in four forms, namely: AEdb-Sequence (sequence and properties of alternatively splice exons), AEdb-Function (data on functional aspects of alternative splicing), AEdb-motif (data and sequence of known splice regulatory motifs), and AEdb-minigene (a collection of known minigene constructs for alternative splice events).

Other satellite databases generated by the members of the ASD consortium will be posted in due course. Currently, the computationally generated AltSplice database has been integrated with the manually curated database of AEdb. This integration adds the value of evidence to computationally predicted isoform splice events.

ProSAS

http://services.bio.ifi.lmu.de/ProSAS

Description :
Protein Structure and Alternative Splicing: effects of alternative splicing events on protein structure

AS-ALPS

http://as-alps.nagahama-i-bio.ac.jp/

Description :
Alternative Splicing-induced Alteration of Protein Structure

ExDom

http://66.170.16.154/ExDom/

Description :
Exon-intron structure of protein domains in seven eukaryotic genomes

Alternative Splicing Database (ASD) Project

http://www.ebi.ac.uk/asd/

Description :
Access to the AltSplice, AltExtron and AEdb databases.

AsiDesigner

http://sysbio.kribb.re.kr/AsiDesigner/

Description :
AsiDesigner is a design software system for siRNA design, that takes into account alternative splicing for mRNA level gene silencing. The software also has the capacity to design siRNAs for silencing of multiple mRNAs simultaneously, to score the performance of designed siRNAs, to search for off-targets with BLAST and FASTA algorithms, and to check for secondary structure energy of siRNAs.

ASDB - Alternative Splicing Database

http://cbcg.lbl.gov/asdb

Description :
ASDB consists of two divisions, ASDB(proteins), which contains amino acid sequences, and ASDB(nucleotides) with genomic sequences. The protein entries from SwissProt are joined into clusters corresponding to alternatively spliced variants of one gene. The DNA division consists of complete genes with alternative splicing mentioned or annotated in GenBank. The search engine allows one to search over SwissProt and GenBank fields and then follow the links to all variants.

ASHESdb

http://sege.ntu.edu.sg/wester/ashes/

Description :
Alternatively spliced human genes by exon skipping database

ATD

http://www.ebi.ac.uk/atd/ The ATD database holds data regarding transcript patterns in human and mouse. A computational pipeline infers exon location on the genome by aligning transcript sequences from the EMBL-Bank database to genomic sequences gathered from the Ensembl database. Annotation manually collected from the available literature adds value to the automatically generated information. The web site also provides a set of computational tools that allow to analyse a particular sequence for the presence of various splicing-related features and to identify tissue-specific splice events.
We have also investigated which splicing events are conserved between the Human and Mouse transcriptome based on the sequence of splice junctions.

EASED - Extended Alternatively Spliced EST Database

http://eased.bioinf.mdc-berlin.de/ EASED is a database of predicted alternative splice forms (ASforms). ASforms are defined by comparing high-scoring ESTs with mRNA sequences using BLAST, taking known exon-intron information (from the ENSEMBL database). Filtering programs compare the ends of each aligned sequence pair for deletions or insertions in the EST sequence, which indicate the existence of alternative splice forms with respect to the exon-intron boundaries. Moreover, we defined the alternative splice profile of each sequence. It indicates the number of alternatively spliced ESTs (NAE), the number of constitutively spliced ESTs (NCE) as well as the number of alternative splice sites (NSS) per mRNA. NAE and NCE correspond to the EST coverage and can be used as a quality indicator for the predicted alternative splice variants. The NSS value specifies the splice propensity of a gene.

Additionally, the tissue type information of all ESTs was included. This allows (a) restriction of the search to certain tissues and (b) calculation of the tissue-NAEs, tissue-NCEs and tissue-NSS. These scores are suitable for the estimation of tissue specificity of certain ASforms. Furthermore, the developmental stage and disease information of the ESTs is available. EASED is accessible at http://www.bioinf.mdc-berlin.de/splice/db/

EDAS - EST-Derived Alternative Splicing Database

http://www.ig-msk.ru:8005/EDAS/

Description :
EDAS is a database of alternative splicing derived from the anlaysis of genomic, protein, mRNA and EST data. It provides classification of elementary alternatives into main types, combined searches for specific alternative variants over tissues and disease states, curated classification of cancer-derived clone libraries by origin (cell line or primary donor tissue), a convenient user interface with in-scale and schematic representation of the alternative exon-intron structure, and a possibility to filter data by the reliability of sources.

Aknowledgement :
We are grateful to Alexey Kazakov and Alexey Fedorov for useful discussion, Pavel Novichkov for programming advice, and Igor Erokhin for comments on the tissue classification. This study was supported by grants from the Howard Hughes Medical Institute (55000309), the Ludwig Institute for Cancer Research (CRDF RB0-1268), the Russian Fund of Basic Research (04-04-49361), and Programs of the Russian Academy of Sciences ("Origin and Evolution of the Biosphere" and "Molecular and Cellular Biology").

References :
1. Nurtdinov, R.N., Artamonova, I.I., Mironov, A.A., and Gelfand, M.S. (2003) Low conservation of alternative splicing patterns in the human and mouse genomes. Hum. Mol. Genet. 2003, 12: 1313-1320.
2. Mironov, A.A., Novichkov, P.S., and Gelfand, M.S. (2001) Pro-Frame: similarity-based gene recognition in eukaryotic DNA sequences with errors. Bioinformatics, 17, 13-15.
3. Mironov, A.A., Fickett, J.W., and Gelfand, M.S. (1999) Frequent alternative splicing of human genes. Genome Res. 1999, 9: 1288-1293.
4. Nurtdinov, R.N., Neverov, A.D., Favorov, A.V., Mironov, A.A., and Gelfand, M.S. (2007) Conserved and species-specific alternative splicing in mammalian genomes. BMC Evol Biol. 2007 7:249.

EID: Exon-Intron Database

http://www.meduohio.edu/bioinfo/eid/

Description :
The Exon-Intron Database (EID), publicly available since 2000, is a flat-file, Fasta-formated collection of sequences and annotations for all exons and introns obtained from GenBank. The primary goal of EID is to offer a comprehensive and convenient dataset of sequences for computational biologists who study exon-intron gene structures and pre-mRNA splicing. New innovations in EID have been implemented in 2005. The collection of exons and introns has been extended beyond coding regions and current versions of EID contain data on untranslated regions of gene sequences as well. Intron-less genes are included as a special part of EID. For species with entirely sequenced genomes, species-specific databases have been generated. Currently, these species-specific sets of all introns and all exons are available for human, mouse, rat, dog, chicken, zebrafish, fruit fly, worm (C. elegans), and mouse-ear cress (A. thaliana). This list will be extended on a monthly basis in accordance with GenBank updates. EID is freely available at http://www.meduohio.edu/bioinfo/eid/.

Recent develoments :
All recent improvements in EID are described in http://www.meduohio.edu/bioinfo/eid/word/README_Sept05.DOC

Aknowledgement :
Support for this work was provided by the Medical University of Ohio Foundation and the Stranahan Foundation, through the Program in Bioinformatics and Proteomics/Genomics. We would like to thank Robert Blumenthal and Peter Bazeley, Medical University of Ohio, for discussion and suggestions on our database.

References :
1. Saxonov, S., Daizadeh, I., Fedorov, A. and Gilbert, W. (2000) EID: The Exon-Intron Database: An exhaustive database of protein-containing genes. Nucl. Acids Res., 28, 185-190.
2. Fedorov, A., Stombaugh, J., Harr, M.W., Yu, S., Nasalean, L. and Shepelev, V. (2005) Computer identification of snoRNA genes using a Mammalian Orthologous Intron Database. Nucl. Acids Res., 33, 4578-4583.

ExInt

http://sege.ntu.edu.sg/wester/exint/

Description :
Exon-intron structure of eukaryotic genes

FUGOID

http://wnt.cc.utexas.edu/~ifmr530/introndata/main.htm/

Description :
Introns in organelle genomes demonstrate wide variation in both features and behavior in Nature. Three classes of organelle introns are now recognized: 1) Group I, 2) Group II, and 3) Group III which are related to Group II introns. These introns have attracted considerable attention because of two remarkable properties: 1) the ability to self-splice, 2) the ability to function as mobile elements. These properties are being explored in order to understand gene evolution and as potential tools in genetic engineering and genomic analysis

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