Modules configuration

It should be noted that in all cases the project directory (dir=) must be declared. Moreover, if SEDA-CLI operations are used, the SEDA version (SEDA=) should be declared as well.

BLAST

blastn

This module accepts as input one or multiple FASTA files, and returns (if there is at least one significant hit) a FASTA file for each input file, containing all sequences showing a significant blastn (https://blast.ncbi.nlm.nih.gov/doc/blast-help/downloadblastdata.html) hit. The query (blastn_query=) and expect (blastn_expect=) parameters must be specified in two separate lines, in the config file. SEDA-CLI operations ([1]; https://hub.docker.com/r/pegi3s/seda/) are performed to remove line breaks from sequences.

tblastn

This module accepts as input one or multiple FASTA files, and returns (if there is at least one significant hit) a FASTA file for each input file, containing all sequences showing a significant tblastn (https://blast.ncbi.nlm.nih.gov/doc/blast-help/downloadblastdata.html) hit. The query (tblastn_query=) and expect (tblastn_expect=) parameters must be specified in two separate lines, in the config file. SEDA-CLI operations ([1]; https://hub.docker.com/r/pegi3s/seda/) are performed to remove line breaks from sequences.

tblastx

This module accepts as input one or multiple FASTA files, and returns (if there is at least one significant hit) a FASTA file for each input file, containing all sequences showing a significant tblastx (https://blast.ncbi.nlm.nih.gov/doc/blast-help/downloadblastdata.html) hit. The query (tblastx_query=) and expect (tblastx_expect=) parameters must be specified in two separate lines, in the config file. SEDA-CLI operations ([1]; https://hub.docker.com/r/pegi3s/seda/) are performed to remove line breaks from sequences.