%# vim: set syntax=mason: <%method title>MSF Intranet - Software written by Aenoch

<& SELF:title &>

Aenoch has written lots of small programs to help peple analyze their data. Most of these are perl scripts which run on the command line. They were written for Linux but will run on Macintosh and Windows computers. Please contact Aenoch if there is a program on this list you would like to use or there is a program you would like written.

% $n = 1; % foreach $key ( sort {$a<=>$b} keys %programs ) { % }
Program Version Description
<% $programs{$key}{'program'} %> <% $programs{$key}{'version'} %> <% $programs{$key}{'description'} %>
<%once> my ( $key, $i, $n, @jc ) = (); my @bgcolor = ( "#ffffff", "#d0d0d0" ); my %programs = ( 1 => { program => "PeaklistMGF.pm", version => "0.02", description => "Object-oriented Perl module for the manipulation of Mascot Generic Format peaklist files.", }, 2 => { program => "calcAverages.pl", version => "0.9.5", description => "Perform basic statistics of experiments using iTRAQ quantitative analysis.", }, 3 => { program => "extract_fasta.pl", version => "", description => "Scan through a large FASTA file and extract only those entries which match a list of characteristics. Can be a list of accession numbers or regular expressions.", }, 4 => { program => "flattenAndPoolMascotDaemonOutput.pl", version => "0.5", description => "Convert a Mascot search result HTML page into a tab-delimited file. Also as the ability to pool together proteins that only differ by one peptide match. But, no one in the group is using Mascot to search their data, right?", }, 5 => { program => "preProcessPeaklist.pl", version => "0.3", description => "Attempt to remove isotope peaks from an MGF peaklist using very simple rules.", }, 6 => { program => "findModifiedPeaklists.pl", version => "0.5", description => "Scan through an MGF peaklist and identify ones that have a neutral loss peak and a corresponding oxonimum peak. Intended for O-GlcNAc.", }, 8 => { program => "mergeDtaIntoMgf.pl", version => "0.3.1", description => "Merge an entire directory of DTA peaklists into a single MGF file for Protein Prospector searching.", }, 9 => { program => "dump_search_compare.pl", version => "0.2.3", description => "Given a project/results_name from Protein Prospector, this script can dump the search compare output into a tab delimited format. It can set almost all the normal SearchCompare options on the command line. Also has the ability to output the MS-Product information for each peptide in the same tab-delimited file.", }, 10 => { program => "exclusion_list.pl", version => "0.2", description => "Given a project/results_name from a Protein Prospector search, return an exclusion list of the peptides already seen.", }, 11 => { program => "extract_xcalibur_excel_quan.pl", version => "0.01.2", description => "Xcalibur can output excel spreadsheets with quantitative information from the MS-level scans. The output is a workbook with multiple sheets. Extract the values from the quantitative analysis from one or more workbooks with one or more sheets into a tab-delmited file.", }, 12 => { program => "extract_accession_to_gene_name.pl", version => "0.1", description => "Read in a SwissProt or UniProt xml database file and extract for each entry all the accession numbers and output a lookup table with the accession number and gene name.", }, 13 => { program => "mapToNewAccession.pl", version => "0.2.0", description => "Takes two files, one a tab-delimited file the other a mapping between one accession number and another. Creates a new column for the lookup value from the mapping table.", }, 14 => { program => "extractUniRefClusters.pl", version => "0.3", description => "Read a UniRef XML library and flatten the cluster information into a single table with the representative member accession number in the first column then the member accession numbers concatected together in the second column.", }, 15 => { program => "parse_go.pl", version => "0.2.2", description => "Add GO annotations to a tab-delimited search compare output.", }, 7 => { program => "find_neutral_loss.pl", version => "0.2.0", description => "Take a list of Peaklist files (.mgf) and look for peaklists that have had a neutral loss of a post-translational modification, or a neutral loss of a charge-reduced species. Output either the matched peaklists or a list of fractions/precursor-charge to be used a s filter for ETD files. Can also do the filtering.", }, # 1 => { program => "", # version => "", # description => "", # }, );