http://wiki.christophchamp.com/index.php?action=history&feed=atom&title=List_of_SEALS_programs 2026-04-30T16:38:43Z Revision history for this page on the wiki MediaWiki 1.26.2 http://wiki.christophchamp.com/index.php?title=List_of_SEALS_programs&diff=3899&oldid=prev 2007-05-04T06:54:22Z

<p></p> <p><b>New page</b></p><div>''Note: system-dependent portions of the documentation are generated on the fly, so some sections of the static web documents may not agree with the documentation produced on your system.''<br /> <br /> ==man pages==<br /> ;gref<br /> ;grefmatrix<br /> ;grefre<br /> ;rwidget<br /> <br /> ==BLAST scripters==<br /> <br /> ;splat : a BLAST scripter<br /> ;:*splatp wusplatp splatpgp<br /> ;:*splatn wusplatn splatngp<br /> ;:*splatx wusplatx splatxgp<br /> ;:*tsplatn twusplatn tsplatngp<br /> ;:*tsplatx twusplatx tsplatxgp<br /> <br /> ;splish : a BLAST scripter<br /> ;:*splishp wusplishp splishpgp<br /> ;:*splishn wusplishn splishngp<br /> ;:*splishx wusplishx splishxgp<br /> ;:*tsplishn twusplishn tsplishngp<br /> ;:*tsplishx twusplishx tsplishxgp<br /> <br /> ;desplat : clean up those messy splat searches<br /> <br /> <br /> ==other scripters/wrappers==<br /> <br /> ;clustalify : wrapper for ClustalW alignment/tree-building program<br /> ;coilify : wrapper for coils2 coiled-coil prediction by NCBI implementation<br /> ;hmm_align : wrapper for HMMER alignment programs<br /> ;hmm_search : database searches based on hidden markov models (wrapper for HMMer programs)<br /> ;lupas_coilify : wrapper for coils2 coiled-coil prediction by Lupas' implementation<br /> ;phdify : wrapper for PHD protein prediction<br /> ;segify : wrapper for SEG low-information domain detection<br /> ;signalpify : wrapper for signalP signal peptide prediction<br /> <br /> ==BLAST result manipulation==<br /> <br /> ;blast2blast : filter any kind of BLAST outputs by score, p : or e-value, etc.<br /> ;blast2bounded : extract HSPs / alignments from BLAST outputs<br /> ;blast2gi : convert BLAST results to lists or tables of hits<br /> ;blast2filename : convert BLAST results to lists or tables of hits<br /> ;blast2header : strip alignment/HSP data from BLAST files<br /> ;gp2normal : make gp variant outputs look more like old-style BLAST<br /> ;psi2normal : filter any kind of BLAST outputs by score, p : or e-value, etc.<br /> ;shatterblast : split/rename BLAST outputs according to query definition line<br /> <br /> ==simple fasta file manipulation==<br /> <br /> ;assign_subversive_gis : assign fake gi numbers to fasta records<br /> ;columnize : format fasta records into columns<br /> ;daffy : You must be taller than this script to ride this ride.<br /> ;defkeys : see the numbering of fasta defline fields<br /> ;faand : find the logical intersection between fasta libraries<br /> ;faclean : remove funny characters from fasta records<br /> ;facount : count the records in fasta libraries<br /> ;fafilt : filter out amino-acid or nucleic-acid sequences<br /> ;faframe : convert a nucleic acid sequence to various possible reading frames<br /> ;faletters : count the letters in fasta libraries<br /> ;falower : convert fasta records to lower case<br /> ;faor : find the logical union between fasta libraries<br /> ;fanot : find the logical difference between fasta libraries<br /> ;fashuffle : shuffle fasta records<br /> ;fasort : sort fasta libraries based on sequences or defline fields<br /> ;fatweak : tweak sequence boundaries<br /> ;fauniq / nrify : remove duplicate fasta records<br /> ;faupper : convert fasta records to upper case<br /> ;faxor : find the logical exclusive union between fasta libraries<br /> ;fenestrate : make windows on fasta records<br /> ;gref : match patterns in fasta libraries<br /> ;mask_split : split fasta records at masking boundaries<br /> ;one2three : convert single-letter amino acid codes to three-letter codes<br /> ;remove_subversive_gis : remove fake gi numbers from fasta records<br /> ;select_defline : select one of multiple deflines in fasta libraries<br /> ;shatter : split/rename fasta records based on the definition line<br /> ;sieve : remove long entries from fasta libraries<br /> ;three2one : convert three-letter amino acid codes to single-letter codes<br /> <br /> ==GenBank flatfile manipulation==<br /> <br /> ;feature2fasta : create fasta records from flatfile features<br /> <br /> ==boundtable manipulation==<br /> <br /> ;blast2bounded : extract HSPs / alignments from BLAST outputs<br /> ;boundtable2fasta : convert tables of sequence fragments into fasta libraries<br /> ;compare_boundtable : compare tables representing sequence fragments; find overlaps<br /> ;merge_boundtable : merge tables of sequence fragments<br /> ;project_boundtable : project normal and complement elements onto a single strand<br /> ;split_boundtable : split discontinuous sequence fragments<br /> ;standardize_boundtable : convert boundtables of different formats to the canonical SEALS format<br /> ;strip_boundtable : strip normal or complement elements from boundtables<br /> <br /> ==Entrez retrieval==<br /> <br /> ;entrezping : test your Entrez server<br /> ;gi2abstract : find abstracts associated with sequences<br /> ;gi2fasta : retrieve sequence data for a gi number<br /> ;gi2genbank : retrieve sequence data for a gi number<br /> ;gi2asn1 : retrieve sequence data for a gi number<br /> ;gi2defline : retrieve sequence data for a gi number<br /> ;gi2genbank_html : retrieve sequence data for a gi number<br /> ;genome2gi : find all sequences from a systematic sequencing / mapping project<br /> ;taxnode2amino_gi : get all gis associated with a taxnode<br /> ;taxnode2gi : get all gis associated with a taxnode<br /> ;taxnode2nucleic_gi : get all gis associated with a taxnode<br /> <br /> ==Netscape / html==<br /> <br /> ;hotbr : html-ify BLAST outputs<br /> ;hotgi : hotlink gi numbers in any file<br /> ;liftscape : raise the current default Netscape window<br /> ;peepscape : grab the URL from a Netscape window<br /> ;pipescape : pipe a file into Netscape<br /> ;pipescape_new : pipe a file into Netscape<br /> ;spitscape : spit out the text from a Netscape window<br /> <br /> ==pattern matching==<br /> <br /> ;gref : match patterns in fasta libraries<br /> ;grefd : match patterns in fasta libraries<br /> ;guess : guess a pattern from an alignment<br /> ;prosite2perl : translates PROSITE-style regular expressions into Perl<br /> ;prosite_as_perl : search PROSITE by text word, returning perlish patterns<br /> <br /> ==taxonomy analysis==<br /> <br /> ;tax_break : summarize taxonomy data for a list of gi numbers<br /> ;tax_collector : summarize taxonomic identity of nearest homologs<br /> ;tax_filt : filter gi numbers according to taxonomy<br /> ;tax_guess : find an exact taxonomic name<br /> ;tax_validate : validate that the ranks in the taxonomy are consistent<br /> ;taxnode2lineage : see the lineage of any taxonomic node<br /> <br /> ==unipred==<br /> <br /> ;coil_table : create a table of predicted coiled-coil domains using ccp<br /> ;seg_table : create a table of predicted nonglobular domains using SEG<br /> ;sig_table : create a table of predicted signal peptides using SignalP<br /> ;tm_table : create a table of predicted transmembrane domains using PHD<br /> ;unipred : predict structural domains<br /> <br /> ==general converters/extractors==<br /> <br /> ;boundtable2fasta : convert tables of sequence fragments into fasta libraries<br /> ;blastalign2fasta : convert blast alignments to aligned fasta records<br /> ;block2fasta : convert aligned sequence blocks to aligned fasta records<br /> ;clustalign2fasta / clustal2fasta : convert CLUSTALW alignments into aligned fasta format<br /> ;defline2gi : extract gi numbers from the deflines of fasta records<br /> ;fasta2clustalign : convert aligned fasta records to CLUSTALW format.<br /> ;fasta2defline : extract the definition lines of fasta records<br /> ;fasta2gi : extract gi numbers from the deflines of fasta records<br /> ;fasta2phylip : convert aligned fasta records to PHYLIP format.<br /> ;fasta2selex : convert aligned fasta records to SELEX format.<br /> ;fasta2seqrows : convert fasta records to sequence rows<br /> ;fastalign2fasta : remove special delimiters from aligned fasta records.<br /> ;fastalign2hmm : convert aligned fasta records into a format compatible with HMMER<br /> ;genbank2gi : extract gi numbers from GenBank records<br /> ;hmm2gi : extract gi numbers from HMMER searches<br /> ;hmmalign2fasta : convert HMMER alignments into aligned fasta records<br /> ;macaw2fasta : convert MACAW alignments into aligned fasta format<br /> ;most2gi : extract gi numbers from MoST outputs<br /> ;phylip2fasta : convert PHYLIP alignments to aligned fasta records<br /> ;selex2fasta : convert SELEX alignments into aligned fasta format<br /> ;seqrows2fasta : convert sequences from sequence-row format to fasta records<br /> <br /> ==miscellaneous functions==<br /> <br /> ;agree : create a consensus sequence from an alignment<br /> ;casealign2count : substitute length values for unaligned regions in alignments<br /> ;deindex : cleans up index files created by fasta2index<br /> ;fasta2index : make indexes of fasta libraries for fast retrieval<br /> ;famask : mask fasta libraries based on predicted structural domains<br /> ;gap_cds : insert gaps in nucleotide sequence based on amino-acid alignments<br /> ;gi2sibling : find siblings for nucleotide and protein records<br /> ;grouper : group sequences by similarity scores<br /> ;purger : group sequences by similarity scores<br /> ;wimklein : a versatile translator<br /> ;wubwub : find duplications within a sequence<br /> <br /> ==administration==<br /> <br /> ;seals : examine your SEALS status<br /> <br /> ;update_blastgp : update BLAST-GP from the NCBI ftp site<br /> ;update_gi_lists : update retrieval hints from the NCBI ftp site<br /> ;update_modules : update Perl modules from a CPAN site<br /> ;update_perlpath : set the correct perl interpreter for SEALS scripts<br /> ;update_permissions : set permissions and links for your SEALS installation<br /> ;update_prosite : update the local PROSITE database from the Expasy web site<br /> ;update_seg : update SEG from the NCBI ftp site<br /> ;update_taxonomy : updates the local taxonomy databases from the NCBI ftp site<br /> ;update_wublast : update WU-BLAST from the Washington University ftp site<br /> <br /> ==generic scripters==<br /> <br /> ;foreach_blast : run a command on a series of BLAST results<br /> ;foreach_fasta : run a command on a series of fasta records<br /> ;foreach_file : run a command on a series of directories<br /> ;foreach_genbank : run a command on a series of GenBank-style flatfiles<br /> ;foreach_dir : run a command on a series of directories<br /> ;foreach_line : run a command on a series of lines<br /> ;foreach_paragraph : run a command on a series of empty line-delimited paragraphs<br /> ;foreach_word : run a command on a series of words<br /> <br /> ==general utilities==<br /> <br /> ;bert : a cat, with enormous globs<br /> ;dupedupe : find duplicate lines<br /> ;mailme : send a note to myself<br /> ;nemp : n e match print<br /> ;pathadd : add/remove path elements<br /> ;plainwhich : simple 'which' replacement<br /> ;sortby : sort lines according to a reference set<br /> ;uniquniq : create files of unique lines<br /> ;singsing : find unduplicated lines<br /> ;stack_paragraphs : stack paragraphs onto single lines<br /> ;unstack_paragraphs : unstack single lines into paragraphs<br /> <br /> ==logical operations==<br /> <br /> ;and : find the logical intersection between lines in files<br /> ;not / nor : find the logical difference between lines in files<br /> ;or : find the logical union between lines in files<br /> ;xor : find the logical exclusive union between lines in files<br /> ;faand : find the logical intersection between fasta libraries<br /> ;fanot : find the logical difference between fasta libraries<br /> ;faor : find the logical union between fasta libraries<br /> ;faxor : find the logical exclusive union between fasta libraries<br /> <br /> [[Category:SEALS| ]]</div>

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