To create personalized sequence databases for proteogenomics (single amino acid variants, splice junctions).To combine multiple sequence databases by concatenating.This is particularly helpfulįastaManipulator (Perl script, ) To report summarized content of a sequence database using the index numbers of each entry.To append, via web UI, user provided sequences (fusion constructs, contaminants, etc).Than searches performed on complete databases. Searches performed on these smaller subset databases are often very much faster To create subset sequence databases based on either a Species/Protein Molecular Weight pre-filter.Accelerate searches that are pre-filtered by intact protein MW and/or species.Generation purposes, thus decreasing memory requirements for program execution. Hit is recorded during a search, then later use that number for rapid retrieval of that database entry for output/report Enable an internal means for Spectrum Mill programs to store an index number when a.fasta file based on accession number, species, and protein mw, which: Spectrum Mill programs rapid, byte-specific access to a. To create several indexes much smaller files than a FASTA sequence database file itself.The SM Protein Sequence Database Utilities web page provides access to several key capabilities enabled by a few different programs and scripts: FAindex (C++ program, faindex.cgi) Personalized Sequence Databases for proteogenomics (single amino acid variants, splice junctions).Links to related topics in separate stand-alone documents: Changing the HTML Link from the Accession Number in the Search.
Links to related topics in the general and server administration instructions:
Translate nucleotide FASTA to protein FASTA.Create subset FASTA database from Species and Protein MW.Create subset FASTA database from Accession Numbers.for Proprietary/Generic FASTA Databases.Spectrum Mill supported FASTA Database Header Formats.Obtaining and Updating Sequence Databases.Protein Sequence Database Help Spectrum Mill
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