Authors Eric Fontanillas created the version 1 of this pipeline. Victor Mataigne developped version 2.

Galaxy integration Julie Baffard and ABiMS TEAM, Roscoff Marine Station

Contact support.abims@sb-roscoff.fr for any questions or concerns about the Galaxy implementation of this tool.

Credits : Gildas le Corguillé, Misharl Monsoor

Description

This tool takes files containing nucleic aligned sequences and search the ORF and the CDS.

Inputs

Input files : (multiple) fasta files with nucleic aligned sequences.

Parameters

• methionine : choose to consider the methionine in the search of CDS.

  yes/no.

• 'Minimal number of species in each locus'

  Default : 10 (integer).

• 'min_length_seq' :

  minimal length of the sequence (in amino acids). when the removal of the indel is done, the minimal length equals : previous length - 20. for example if you choose 50 for the minimal length, the actual length equals 30. Default : 50 (integer).

• 'min_length_subseq' :

  minimal length of the subsequence (in amino acids). subsequence means the part of the original sequence between 2 sets of indels. an indel set is composed by more than 2 indels, if not the set is considered as unknown amino acid. Default : 15 (integer).

• 'min_length_nuc' :

  Minimal length of the sequence in the nucleic format, without indels. Default : 50 (integer).

• others parameters allowing to choose which outputs you desire :

  • outputs with best ORFs.
  • outputs with CDS, with or without indels.
  • in proteic or nucleic format.

Outputs

• ORF_Search

  the log file (mainly statistics about the tool).

• ORF_Search_Best_ORF_aa

  the output with the best ORF in the proteic format.

• ORF_Search_Best_ORF_nuc

  the output with the best ORF in the nucleic format.

• ORF_Search_CDS_aa

  the output with the CDS (regardless the Methionine) in the proteic format.

• ORF_Search_CDS_nuc

  the output with the CDS (regardless the Methionine) in the nucleic format.

• ORF_Search_CDS_with_M_aa

  the output with the CDS (considering the Methionine) in proteic format. the rule : they must have a methionine before the minimal length of the sequence. for example before the 30 last amino acid.

• ORF_Search_CDS_with_M_nuc

  the output with the CDS (considering the Methionine) in nucleic format. the rule : they must have a methionine before the minimale length of the sequence. for example before the 30 last amino acid.

• ORF_Search_CDS_without_indel_aa

  is the output with the CDS without indel in proteic format. considering the Methionine or not : according to the option chosen.

• ORF_Search_CDS_without_indel_nuc

  is the output with the CDS without indel in proteic format. considering the Methionine or not : according to the option chosen.

The AdaptSearch Pipeline