| 1 |
CONTRAST - CONditionally TRAined Search for Transcriptshttp://contra.stanford.edu/contrast/ |
| Predicts protein-coding genes from a multiple genomic alignment. It is designed for de novo predictions. It can also incorporate information from EST alignments. |
| | Gross SS, Do CB, Sirota M, Batzoglou S. CONTRAST: a discriminative, phylogeny-free approach to multiple informant de novo gene prediction. Genome Biol. 2007;8(12):R269. PubMed PMID: 18096039; PubMed Central PMCID: PMC2246271.
|
| 2007 | 1 |
Predicitions downloadable or can be browsed by using UCSC genome browser.
Predicitions downloadable or can be browsed by using UCSC genome browser. |
| 2 |
ECgenehttp://genome.ewha.ac.kr/ECgene |
| | Lee Y, Lee Y, Kim B, Shin Y, Nam S, Kim P, Kim N, Chung WH, Kim J, Lee S.
ECgene: an alternative splicing database update. Nucleic AcIDs Res. 2007
Jan;35(Database issue):D99-103. Epub 2006 Nov 28. PubMed PMID: 17132829; PubMed
Central PMCID: PMC1716719.
|
| 2006 | 98 |
URL working but not leading to any result page after the query has been given.
URL working but not leading to any result page after the query has been given. |
| 3 |
BLAT - BLAST like Alignment toolhttp://genome.ucsc.edu/cgi-bin/hgBlat?command=start |
| | Kent WJ. BLAT--the BLAST-like alignment tool. Genome Res. 2002
Apr;12(4):656-64. PubMed PMID: 11932250; PubMed Central PMCID: PMC187518.
|
| 2002 | 99 |
1) Link to UCSC Genome browser is given. 2) Splice Sites are marked in the sequence itself, with light blue colour.
1) Link to UCSC Genome browser is given. 2) Splice Sites are marked in the sequence itself, with light blue colour. |
| 4 |
C-Ithttp://C-It.mpi-bn.mpg.de |
| | Gellert P, Jenniches K, Braun T, UchIDa S. C-It: a knowledge database for tissue-enriched genes. Bioinformatics. 2010 Sep 15;26(18):2328-33. Epub 2010 Jul
13. PubMed PMID: 20628071.
|
| 2010 | 99 |
1) Search results downloadable. 2) Gives links to all the pubmed articles mentioning the queried gene
1) Search results downloadable. 2) Gives links to all the pubmed articles mentioning the queried gene |
| 5 |
ASAP II - Alternative Splicing Annotation Projecthttp://bioinfo.mbi.ucla.edu/ASAP2/ |
| | Kim N, Alekseyenko AV, Roy M, Lee C. The ASAP II database: analysis and
comparative genomics of alternative splicing in 15 animal species. Nucleic AcIDs
Res. 2007 Jan;35(Database issue):D93-8. Epub 2006 Nov 15. PubMed PMID: 17108355;
PubMed Central PMCID: PMC1669709.
|
| 2006 | 100 |
1) Gives Genomic expression. 2) Gives Genomic location, gene aliases etc. as gene information. 3) Orthologous genes identified by MULTIZ alignments are given. 4) Isoform sequences are given. 5) Type of exons- Alternative or Constitute are given along with genomic position and number of EST and mRNA observed. 6) Intron type- Alternative or Constitutive, 5 site, 3 site, whether canonical or not and splice type, all information is provided. 7) Alternative Splicing information is provided.
1) Gives Genomic expression. 2) Gives Genomic location, gene aliases etc. as gene information. 3) Orthologous genes identified by MULTIZ alignments are given. 4) Isoform sequences are given. 5) Type of exons- Alternative or Constitute are given along with genomic position and number of EST and mRNA observed. 6) Intron type- Alternative or Constitutive, 5 site, 3 site, whether canonical or not and splice type, all information is provided. 7) Alternative Splicing information is provided. |
| 6 |
GeneNesthttp://genenest.molgen.mpg.de/ |
| GeneNest is a comprehensive visualization of gene indices of the organisms. The aim of GeneNest is to represent each gene by a single cluster of ESTs and/or mRNAs. |
| | Haas SA, Beissbarth T, Rivals E, Krause A, Vingron M. GeneNest: automated generation and visualization of gene indices. Trends Genet. 2000
Nov;16(11):521-3. PubMed PMID: 12199289.
|
| 2000 | 100 |
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| 7 |
PolyA_DB 2http://polya.umdnj.edu/PolyA_DB2 |
| It specializes in identification of Poly-A tail. |
| | Lee JY, Yeh I, Park JY, Tian B. PolyA_DB 2: mRNA polyadenylation sites in vertebrate genes. Nucleic AcIDs Res. 2007 Jan;35(Database issue):D165-8. PubMed PMID: 17202160; PubMed Central PMCID: PMC1899096. |
| 2007 | 100 |
URL not working as on 14 Dec 2012
URL not working as on 14 Dec 2012 |
| 8 |
Rescue-ESEhttp://genes.mit.edu/burgelab/rescue-ese/ |
| | Fairbrother WG, Yeo GW, Yeh R, Goldstein P, Mawson M, Sharp PA, Burge CB. RESCUE-ESE IDentifies candIDate exonic splicing enhancers in vertebrate exons. Nucleic AcIDs Res. 2004 Jul 1;32(Web Server issue):W187-90. PubMed PMID:
15215377; PubMed Central PMCID: PMC441531.
|
| 2004 | 100 |
Gives Exonic Splicing Enhancer motifs.
Gives Exonic Splicing Enhancer motifs. |
