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PAMPA CRAFT: Homology

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touzet edited this page Feb 11, 2025 · 3 revisions

The homology module takes as input a set of target protein sequences, for which peptide markers are unknown, and a set of well-defined peptide markers from related species. Its goal is to identify peptide markers in the target sequences by similarity. For that, the algorithm uses local sequence alignment, allowing up to 10% mismatches. It also checks whether the newly identified peptides can undergo tryptic digestion. Masses and post-translational modifications (PTMs) are computed automatically.

Usage

python3 pampa_craft --homology
   -p PEPTIDE_TABLE [PEPTIDE_TABLE]
                 Peptide table(s) that contain model peptide markers
   -f FASTA      Fasta file for new species
   -d DIRECTORY  Directory containing Fasta files for new species
   -l LIMIT      Limit file that applies to the Fasta sequences.
   -o OUTPUT     Path to the output file (new peptide table)

Example

python3 pampa_craft --homology -p table_A.tsv -f sequences.fasta -o table_B.tsv

This command uses peptide markers from table_A.tsv, matches them to amino-acid sequences in sequences.fasta, and generates a new peptide table, table_B, containing markers corresponding to sequences in sequences.fasta.

Peptide table (-p)

This table contains the list of peptide markers that will be used as models to find new markers in new sequences by homology. The format of this table is described in Peptide tables.

Target sequences (-f, -d and -l)

[Either -f or -d is required. -l is optional] The target sequences are the amino-acids sequences in which the new markers are searched. Those sequences can be available either in a (multi-)FASTA file (-f option), or in a directory containing FASTA files (-d option). In both cases, the set of sequences can optionally be limited to a subset of organisms, molecules or sequence identifiers with -l option.

Option -f : The specified file can contain an arbitrary number of FASTA sequences, coming from various organisms. Refer to the FASTA sequences section for details on the syntax used in FASTA headings.

Option -d: The directory can contain an arbitrary number of FASTA files, following the same requirements as with '-f' option. Only files with extension .fa or .fasta will be examined.

Option -l: This option allows to filter the set of FASTA sequences to limit the selection according to the organism (OS=), the taxid (OX=), the gene name (GN=), the sequence identifier (SeqID=). The full description of the syntax is given in section Limiting searches.

Output file (-o)

This is the name of the new peptide table created by the program, that contains homologous peptide markers.

Example : finding peptide markers for Lutra lutra from the peptide markers of Meles meles

  1. Create a Fasta file containing COL1A1 and COL1A2 sequences for Lutra lutra

Download the file: LutraLutra.fasta

  1. Create a peptide table for the markers of Meles meles.
Taxon Sequence PTM Marker Gene
Meles meles GLPGEFGLPGPAGPR 2H COL1A2-484/B COL1A2
Meles meles GLPGVSGSVGEPGPLGIAGPPGAR 3H COL1A2-793/D COL1A2
Meles meles GLTGPIGPPGPAGAPGDKGEAGPSGPAGPTGAR 2H COL1A1-586/F COL1A1
Meles meles GLTGPIGPPGPAGAPGDKGEAGPSGPAGPTGAR 3H COL1A1-586/F COL1A1
Meles meles GPNGEAGSTGPSGPPGLR 2H COL1A2-292/P2 COL1A2
Meles meles GPPGESGAAGPSGPIGSR 1H COL1A2-502/C COL1A2
Meles meles GPSGEAGTAGPPGTPGPQGLLGAPGILGLPGSR 4H COL1A2-757/G COL1A2
Meles meles GPSGEAGTAGPPGTPGPQGLLGAPGILGLPGSR 5H COL1A2-757/G COL1A2
Meles meles GVQGPPGPAGPR 1H COL1A1-508/P1 COL1A1
Meles meles TGHPGTVGPAGIR 0H COL1A2-978/A COL1A2
Meles meles TGHPGTVGPAGIR 1H COL1A2-978/A COL1A2

Download the file: table_MelesMeles.tsv

  1. Type the command line.
python3 pampa_craft.py --homology -p table_MelesMeles.tsv -f LutraLutra.fasta -o table_LutraLutra.tsv

This creates the result file table_LutraLutra.tsv, that contains new markers for Lutra Lutra.

Download the file: table_LutraLutra.tsv

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