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Filter RefSeq by taxonomy (version 0.3.0+galaxy0)

Choose source of NCBI Taxonomy:

NCBI Taxonomy database:

Choose source of RefSeq sequences:

Select RefSeq FASTA file:

Ancestor taxon (scientific) name:

Exclude curated sequences from dataset:

Curated sequences are identified by their accession number prefixes and excluded if this option is checked

Exclude predicted sequences from the dataset:

Computationally predicted (but not curated) sequences are identifed by their accession number prefix and excluded if this option is checked

This tool allows NCBI RefSeq sequences to be filtered so that only those whose species name are descendants of a given taxon in the NCBI taxonomy are retained. For example, from the NCBI RefSeq "other vertebrate" file only ray finned fishes can be retained by filtering for "Actinopterygii".

The NCBI RefSeq FASTA files can either be provided by the Galaxy administrator or from the user history. The NCBI taxonomy should be provided by the Galaxy administrator but if that is not possible the nodes.dmp and names.dmp files from the NCBI taxonomy can be provided in the history.