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Tools

Tools are in free access Public access or restricted access Registered access

They run on the web, unix or both.

Tools in restricted access can use unpublished data.


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S-MART manages your RNA-Seq and ChIP-Seq data. It also produces many different plots to visualize your data.PresentationSeveral tools are now available for mapping high-throughput sequencing data from a genome, but few can extract biological knowledge from the mapped reads. We have ...

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Short Oligonucleotide Analysis Package
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a short read de novo assembly tool
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an accurate consensus sequence builder
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Genome-wide ab initio detection of splice junction sites from RNA-Seq
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Sam

Sequence alignment and modeling system
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Wide range of tools for alignments in the SAM or BAM format.More information on SourceForge.
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It is a Web-based Libre Software hosting system. It includes issue tracking (bugs, tasks, support, news and documentation), project member management by roles and individual account maintenance.
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A graphical multiple sequence alignment editor
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SignalP 3.0 predicts the presence and location of signal peptide cleavage sites in amino acid sequences from different organisms: Gram-positive prokaryotes, Gram-negative prokaryotes, and eukaryotes. The method incorporates a prediction of cleavage sites and a signal peptide/non-signal peptide prediction based on a combination of ...

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Genomic/cDNA sequence comparison
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Specific Primers & Amplicon Design Software FUNCTIONGENOPLANTETMSPADS tries to design a unique GST (Gene-Sequence Tag) and a specific primer set for its PCR amplification, on a genomic sequence, knowing the gene structure. DESCRIPTIONIn transcriptome approaches, probes corresponding to individual members of multigenic families often lack specificity ...

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Splice Site Prediction (Arabidopsis, Maize)
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Splice Site Prediction (Arabidopsis, Human)
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sequence analysis package (alfsplit,assemble4,gap4 ...)
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Smith Waterman sequence comparison
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Update: 02 Dec 2011
Creation date: 31 May 2011