neXtProt - The knowledge resource on human proteins

This is a code repository for the SIB - Swiss Institute of Bioinformatics CALIPHO group neXtProt project

See: http://www.nextprot.org/

pepx

Peptide matcher across neXtProt entries and variants

To build the application

gcc pepx.c -o pepx

indexing exemple: pepx --IL --ignore-variants -x my_index_folder -b my_sequence_file searching exemple: pepx --IL -x my_index_folder -s NFIVSTWHR

When running the application

Pepx possible arguments are:

• --search (short=-s) to perform a peptide search
• --build (short=-b) to build indexes (requires the isoform-file name as mandatory argument)
• --version (short=-v) to show current version
• --help (short=-h) to show this help
• --index-folder (short=-x) to specify an index folder (default is .)
• --variant-folder (short=-w) to specify a folder for json variants (required for build command when ignore-variants flag is not set)
• --peptide-file (short=-p) a file with peptides to search (1 peptide/line, if not provided peptides will be read from stdin)
• --ignore-variants to build indexes not considering variants
• --IL to build indexes merging I and L and search these indexes
• --7mers-only to build only 7-mer indexes (saves disk space)
• --noiso (short=-n) to output search results at the entry level

Current limitation:

• poly-AA stretches > 7 can not be exactly found and are overpredicted
• only snp-style (1 AA for 1 other AA), and 1-AA-miss variants are accounted
• max 128 variants accounted within a given x-mer
• only 1 joker (X) allowed in a given x-mer in search mode