tide-index

Usage:

tide-index [options] --fasta=<filename>

Description:

The tide-index program converts a FASTA format file of protein sequences into a format that can be read efficiently by tide-search.

Input

• A FASTA file of protein sequences. The input file name is set using --fasta=<filename>.

Output

• Peptide index - By default the name of the peptide index file will be the name of the input FASTA file, but with the suffix .pepix. The peptide index file name can be set using the --peptides option.
• Protein index - by default the name of the protein index file will be the name of the input FASTA file, but with the suffix .protix. The protein index file name can be set using the --proteins option.
• Auxiliary peptide location index. This binary file contains information on where peptides are located within indexed proteins in cases where a peptide appears in more than one location. By default the name of the auxiliary locations index file will be the name of the input FASTA file, but with the suffix .aux_locs. The auxiliary peptide location file name can be set using the --aux_locations option.

Options

• --enzyme=<string> – Specify the enzyme used to digest the proteins in silico. Available enzymes include trypsin, chymotrypsin, elastase, clostripain, cyanogen-bromide, idosobenzoate, proline-endopeptidase, staph-protease, modified-chymotrypsin, elastase-trypsin-chymotrypsin and aspn. Specifying --enzyme=none yields a non-enzymatic digest. Warning: the resulting index may be quite large. Default=none.
• --digestion=full-digest|partial-digest – Specify whether every peptide in the database must have two enzymatic termini (full-digest) or if peptides with only one enzymatic terminus are also included (partial-digest). Default=full-digest
• --max_missed_cleavages – Maximum number of missed cleavages per peptide to allow in enzymatic digestion. If this option is not specified, then missed cleavages are not allowed.
• --max_length=<integer> – Specify the maximum length of the peptides included in the index. Default=50.
• --max_mass=<integer> – Specify the maximum monoisotopic mass (in Da) of the peptides included in the index. Default=7200.
• --min_length=<integer> – Specify the minimum length of the peptides included in the index. Default=6.
• --min_mass=<integer> – Specify the minimum monoisotopic mass (in Da) of the peptides included in the index. Default=200.
• --peptides=<filename> – Specify the name of the output peptide index.
• --proteins=<filename> – Specify the name of the output protein index.
• --monoisotopic_precursor – Use monoisotopic precursor masses rather than average mass (default) for precursor.
• --mods_spec – Expression for static and variable mass modifications to include. Specify a comma-separated list of modification specifications of the form:

  --mods_spec=C+57.02146,2M+15.9949,1STY+79.966331,...

  The general form of a modification specification has 3 components, as exemplified by 1STY+79.966331.

  The three components are:

  [max_per_peptide]residues+added_mass.

  In the exemplar, max_per_peptide is 1, residues are STY, and added_mass is 79.966331.

  • residues indicate which amino acids may be affected by the modification.
  • added_mass indicates in Daltons the mass to add to modified versions of the residues.
  • max_per_peptide indicates how many occurrences of the indicated variable modification may occur per peptide. The max_per_peptide may be omitted, as in C+57.02146, to indicate a static modification, which will be in force at all occurrences of the amino acid residue.

  Notes: Currently only positive mass modifications are specifiable (added_mass > 0). Use caution in specifying variable modifications: specifying many modifications or higher numbers of max_per_peptide can increase index size significantly.

Example:

./tide-index --enzyme=trypsin --mods_spec=C+57.02146 --fasta=yeast.fasta