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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. We can keep you informed of updates if you susbscribe to our low-volume email list - see here.
PartiGene tools, including CLOBB, annot8r and prot4EST | Phylogenomics | DNA barcoding - jMOTU
what |
why |
who currently curates
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The Partigene Suite of transcriptome analysis tools |
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A databasing tool for EST datasets current version 3.0.5 |
Mark Blaxter |
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A tool for processing EST capillary sequencing traces |
Mark Blaxter |
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A tool (derived from trace2dbEST above) for processing all sorts of capillary sequencing traces |
Mark Blaxter |
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A tool for clustering (EST) sequences on the basis of BLAST similarity searches |
John Parkinson and Mark Blaxter |
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Web interface tool for PartiGene databases |
Mark Blaxter |
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A port of our Partigene suite (including trace2dbest) for the Mac OS X 10.4 system |
Mark Blaxter |
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A pipeline for prediction of peptides from neglected genome sequence datasets |
James Wasmuth |
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Annotation of peptide or nucleotide sequences with GO, KEGG and EC tags based on sequence similarity |
Mark Blaxter |
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Annotation of peptide sequences with physical property decriptions |
Mark Blaxter |
Tools for Phylogenomics analyses |
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A Taxonomy database Manager for large phylogenetic datasets |
Martin Jones |
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A tool for finding the Matrix Attachment Region (MAR) Recognition Signature in DNA sequence |
Mark Blaxter |
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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 |
DNA barcode analysis tools |
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java programmes for the analysis of large DNA barcode datasets |
Martin Jones and Mark Blaxter |
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a perl programme for inference of Molecular Operational Taxonomic Units from DNA barcode data [superseded by jMOTU above] |
Mark Blaxter |
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Website Highlight
The filarial nematode Litomosoides sigmodontis.
Filarial nematodes are tissue and gut parasites of a wide range of vertebrates, including humans. This species is a rodent model for species, such as O. volvulus, that cause human diseases, affecting over 120 million people. See NEMBASE4 for analyses of ESTs from this parasite and many other nematodes.
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