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BaNG Nematode and Neglected Genomics |
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| The Blaxter Lab at the Institute of Evolutionary Biology, University of Edinburgh | ||
Bioinformatics Software
A major activity in the Blaxter lab is the development and use of bioinformatics tools to analyse genome sequence data, particularly data relating to comparative, or phylo-, genomics. We have developed new bioinformatic tools for our comparative genomics research, and also use a number of public-domain tools.
[ Some useful scripts and programmes | Please see here for Blaxter Lab Databases | See here for the Ashworth Labs BioCluster pages ]
what
why
who
trace2dbEST A tool for processing EST capillary sequencing traces Alasdair Anthony trace2seq A tool (derived from trace2dbEST above) for processing all sorts of capillary sequencing traces Mark Blaxter & Alasdair Anthony PartiGene A databasing tool for EST datasets Ralf Schmid wwwPartiGene Web interface tool for PartiGene databases Ralf Schmid PartiGene for Mac OSX A port of our Partigene suite (including trace2dbest) for the Mac OS X 10.4 system Mark Blaxter prot4EST A pipeline for prediction of peptides from neglected genome sequence datasets James Wasmuth
annot8r Annotation of peptide or nucleotide sequences with GO, KEGG and EC tags based on sequence similarity Ralf Schmid annot8r_physprop Annotation of peptide sequences with physical property decriptions Ralf Schmid TaxMan A Taxonomy database Manager for large phylogenetic datasets Martin Jones MRSfinder A tool for finding the Matrix Attachment Region (MAR) Recognition Signature in DNA sequence Alasdair Anthony SimiTri A tool for visualising the relative BLAST-based similarity scores for a sequence dataset compared to datasets from other organisms John Parkinson and Mark Blaxter CLOBB A tool for clustering (EST) sequences on the basis of BLAST similarity searches John Parkinson, David Guiliano and Mark Blaxter MOTU_define.pl a programme for inference of Molecular Operational Taxonomic Units from DNA barcode data Mark Blaxter & Robin Floyd Blaxter Lab BLAST server A local installation of the NCBI BLAST toolkit, focussed on nematode genomics analysis Ralf Schmid Downloads Page of software available for download Links Links to users of our bioinformatics software
...other interesting things... 
The parasitic nematode Trichuris muris. T. muris is a gut parasite of mice, and is used as a research model for the human-parasitic T. trichiura. See NEMBASE3 for analyses of ESTs from this parasite and many other nematodes. |
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