miRviewer – Multispecies microRNA Homologous Viewer

miRviewer

:: DESCRIPTION

microRNAviewer presents a global view of homologous miRNA genes in many species.

::DEVELOPER

miRviewer team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

BMC Res Notes. 2012 Feb 13;5:92. doi: 10.1186/1756-0500-5-92.
miRviewer: a multispecies microRNA homologous viewer.
Kiezun A1, Artzi S, Modai S, Volk N, Isakov O, Shomron N.

genBlastA 1.0.4 / genBlastG 1.39 – Homologous Gene Sequences

genBlastA 1.0.4 / genBlastG 1.39

:: DESCRIPTION

genBlast is a program suite, consisting of two programs: genBlastA and genBlastG.

genBlastA parses local alignments, or high-scoring segment pairs (HSPs) produced by local sequence alignment programs such as BLAST and WU-BLAST and identify groups of HSPs. Each HSP group represent a putative gene that is homologous to the query protein (gene).

genBlastG is a fast homology-based gene finder. It builds on genBlastA. In particular, it takes genBlastA output as input and define gene models baesd on the HSP group.

::DEVELOPER

Jack Chen lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX

:: DOWNLOAD

 genBlastA / genBlastG

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Aug 1;27(15):2141-3. doi: 10.1093/bioinformatics/btr342. Epub 2011 Jun 8.
genBlastG: using BLAST searches to build homologous gene models.
She R1, Chu JS, Uyar B, Wang J, Wang K, Chen N.

Genome Res. 2009 Jan;19(1):143-9. doi: 10.1101/gr.082081.108. Epub 2008 Oct 6.
GenBlastA: enabling BLAST to identify homologous gene sequences.
She R1, Chu JS, Wang K, Pei J, Chen N.

Carnac 0.98 – Predict Secondary Structure for a set of Homologous RNA Sequences

Carnac 0.98

:: DESCRIPTION

Carnac is a software tool for analysing the hypothetical secondary structure of a family of homologous RNA. It aims at predicting if the sequences actually share a common secondary structure. When this structure exists, Carnac is then able to correctly recover a large amount of the folded stems. The input is a set of single-stranded RNA sequences that need not to be aligned. The folding strategy relies on a thermodynamic model with energy minimization. It combines information coming from locally conserved elements of the primary structure and mutual information between sequences with covariations too.

Carnac Online Version

::DEVELOPER

Bonsai Bioinformatics – INRIA

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows /  Linux / MacOsX
  • C Complier

:: DOWNLOAD

Carnac

:: MORE INFORMATION

Citation

CARNAC: folding families of related RNAs
Touzet H. and Perriquet O.
Nucl. Acids Res. (2004) 32 (suppl 2): W142-W145