list path, taxonomy information

# list path, taxonomy information ## Syntax Value is an ASCII text string describing a configuration file. ## Notes Relative or absolute path names can be used. If the configuration file are resident on a remote disk, a full UNC path name is usually required. Any allowed file name can be used, but only one taxonomy configuration file can be specified per input. ## Description The parameter is used to pass the location of the file that translates the "taxonomy" information in the value protein, taxon into a list of FASTA file names. A simple taxonomy file is illustrated below.
    <?xml version="1.0"?>
    <bioml label="x! taxon-to-file matching list">
    	<taxon label="human">
    		<file format="peptide" URL="../fasta/human.fasta.pro" />
    		<file format="peptide" URL="../fasta/human_extra.fasta" />
    		<file format="spectrum" URL="../lib/human_fasta.hlf" />
    		<file format="saps" URL="../fasta/human_saps.xml; />
    		<file format="mods" URL="../mods/human_mod.xml" />
    	</taxon>
    	<taxon label="yeast">
    		<file format="peptide" URL="../fasta/scd.fasta.pro" />
    		<file format="peptide" URL="../fasta/scd_1.fasta.pro" />
    		<file format="peptide" URL="../fasta/extras.fasta.pro" />
    	</taxon>
    </bioml>
If the protein, taxon value is set to human, then the files examined by TANDEM to find a matching peptide sequence would be as follows, in the order listed: ../fasta/human.fasta.pro ../fasta/human_extra.fasta The additional files listed for human would be used as follows: The file "../fasta/saps/human_saps.xml" would be loaded in to provide information about known single amino acid polymorphisms. The file "../fasta/mods/human_mod.xml" would be loaded in to provide information about known potential modifications. If X! Hunter was being used, the file "../lib/human_fasta.hlf" would be used to provide annotation spectrum library information. Notes: If a file is listed more than once, it is only used one time. Do not use commas in the labels for taxon entries: all other normal characters are allowed. X! Tandem interprets a comma as separating multiple taxon entries. For example, human,yeast would be interpreted as the union of all of the sequence files in both the human and yeast taxon entries. If a sequence file does not exist, processing continues if at least one sequence file for the taxon does exist. The output file records all of the sequence files actually used: non-existent files are not listed. Avoid using the same taxon label twice in a taxonomy file. If more than one instance of a taxon label is found, the union of all of the sequence files for the multiple instances of that taxon label are used for the calculation. see also: protein, taxon | FASTA-pro format X! TANDEM API description project