:: DESCRIPTION
GIIRA is a gene prediction method that identifies potential coding regions exclusively based on the mapping of reads from an RNA-Seq experiment.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2014 Mar 1;30(5):606-13. doi: 10.1093/bioinformatics/btt577. Epub 2013 Oct 11.
GIIRA–RNA-Seq driven gene finding incorporating ambiguous reads.
Zickmann F1, Lindner MS, Renard BY.
:: DESCRIPTION
mGene is a computational tool for the genome-wide prediction of protein coding genes from eukaryotic DNA sequences. It is based on recent advances in machine learning and uses discriminative training techniques, such as support vector machines (SVMs) and hidden semi-Markov support vector machines (HSMSVMs). Its excellent performance was proved in an objective competition based on the genome of the nematode Caenorhabditis elegans. The evaluated developmental version of mGene exhibited the best prediction performance (in terms of the average between sensitivity and specificity) for the multiple-genome prediction tasks on all four evaluation levels (considering, nucleotides, exons, transcripts and genes). The ab-initio version was best on nucleotide, exon and transcript level, and only slightly worse than Augustus on the gene level. The fully developed version shows the best overall performance compared to the submitted gene finders’ predictions, including the ones of Fgenesh and Augustus.
::DEVELOPER
the Biomedical Informatics Lab
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Schweikert et al.
mGene: accurate SVM-based gene finding with an application to nematode genomes..
Genome Res. 2009 Nov;19(11):2133-43.
:: DESCRIPTION
MetaGeneAnnotator is a prokaryotic gene finding program from environmental genome shotgun sequences or metagenomic sequences.
::DEVELOPER
Hideki Noguchi (hnoguchi @nig.ac.jp)
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
MetaGeneAnnotator: detecting species-specific patterns of ribosomal binding site for precise gene prediction in anonymous prokaryotic and phage genomes.
Noguchi H, Taniguchi T, Itoh T.
DNA Res. 2008 Dec;15(6):387-96. doi: 10.1093/dnares/dsn027.
:: DESCRIPTION
LOCUS (Length Optimized Characterization of Unknown Spliceforms) is a dynamic-programming algorithm for finding the optimal set of splice sites in a genomic region of interest with estimated prior length information.
::DEVELOPER
Stormo Lab in Department of Genetics, Washington University
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2006 May 15;22(10):1239-44. Epub 2006 Apr 4.
Using mRNAs lengths to accurately predict the alternatively spliced gene products in Caenorhabditis elegans.
Agrawal R, Stormo GD.
:: DESCRIPTION
TransGeneScan is a software tool for finding genes in assembled transcripts from metatranscriptomic sequences.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
BMC Bioinformatics. 2014;15 Suppl 9:S8. doi: 10.1186/1471-2105-15-S9-S8. Epub 2014 Sep 10.
Gene finding in metatranscriptomic sequences.
Ismail WM, Ye Y, Tang H.
:: DESCRIPTION
The GotohScan program is a search tool that finds shorter sequences (usually genes) in large database sequences (chromosomes, genomes, ..)by computing all semi-global alignments. Thus, the query sequence is never truncated or split into subsequences, but always mapped to the database over its complete length. The alignment is computed via the Gotoh-alignment algorithm using affine gap costs.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
