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Tools

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Tools in restricted access can use unpublished data.


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BLAST+ NCBI 2.2.29
  • Public BLAST using ViroBLAST interface.
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BWA

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Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively short nucleotide sequences against a long reference sequence such as the human genome. It implements two algorithms, bwa-short and BWA-SW. The former works for query sequences shorter than 200bp and the latter for longer ...

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a flexible suite of utilities for comparing genomic features.
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BioMart is no more maintained at URGI.
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New compact graphical representations have been developed (1) a chromosome cascading zoom allows the user to enlarge a region of chromosome as deep as he needs, while keeping an overview of the whole chromosome map. (2) A new compact QTL track summarizing QTL data ...

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WU-BLAST2 gapped blast and tools.Warning: this software is deprecated and has been replaced by AB-BLAST, which is not available at URGI.
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 The BLASTER suite gathers C++ programs developed for transposable element search and their annotation in large eukaryotic genome sequence. But we think that the tools are generic enough to be used in other contexts. The suite is composed by three programs BLASTER, MATCHER and GROUPER. ...

Fast sequence search command line tool.BLAT on DNA is designed to quickly find sequences of 95% and greater similarity of length 25 bases or more. It may miss more divergent or shorter sequence alignments. It will find perfect sequence matches of 25 bases, and ...

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Blocksearch search for protein motifs or patterns
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An ultrafast, memory-efficient short read alignerIt aligns short DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp reads per hour. Bowtie indexes the genome with a Burrows-Wheeler index to keep its memory footprint small: typically about 2.2 GB ...

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Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences.It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes.Bowtie 2 ...

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BreakDancer-1.1, released under GPLv3, is a Perl/Cpp package that provides genome-wide detection of structural variants from next generation paired-end sequencing reads. It includes two complementary programs.BreakDancerMax predicts five types of structural variants: insertions, deletions, inversions, inter- and intra-chromosomal translocations from next-generation short paired-end sequencing ...

Update: 02 Dec 2011
Creation date: 31 May 2011