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Spaln: align cDNA or Protein to genome (version 2.4.9+galaxy0)

Genome sequence to search (FASTA format):

Query sequence(s) (protein or cDNA):

Output format:

Species to use for parameter setting:

Choose a species table (e.g. cynosemi) from which to read parameters to optimise spaln

Advanced settings:

Spaln (space-efficient spliced alignment) is a stand-alone program that maps and aligns a set of cDNA or protein sequences onto a whole genomic sequence in a single job.

This Galaxy wrapper currently only supports the default (i.e. -O3) algorithm for Spaln. This algorithm takes FASTA format query and genome sequence and finds an alignment of the query (either cDNA or protein) against the genome.

Spaln optionally takes a species name to use for parameter setting (the "-T" parameter). The "List spaln parameter tables" (list_spaln_tables) can be used to find a parameter file that is close (in terms of taxonomic distance) to your species of interest. Use of this setting is recommended.