1527136fc7c7b09cc1e6e74cac0e190d90818e94 max Fri Aug 21 08:40:06 2015 -0700 sorting tools by topic, refs #15113, note 80 diff --git src/hg/hgTracks/extTools.ra src/hg/hgTracks/extTools.ra index aefe656..5e90607 100644 --- src/hg/hgTracks/extTools.ra +++ src/hg/hgTracks/extTools.ra @@ -65,133 +65,30 @@ param chr $s param start $[ param end $] tool primer3Plus shortLabel Primer3Plus longLabel Updated interface of the popular primer designer. Primers flank the nucleotide in the center of the screen. url http://primer3plus.com/cgi-bin/geneBro/primer3plus.cgi email server@untergasser.de maxSize 10000 param GENBRO_RETURN_PATH $returnUrl param GENBRO_DB $db param GENBRO_POSITION $position param SEQUENCE_TEMPLATE $seq -tool nebcutter -shortLabel NEBCutter -longLabel New England Biolabs Restriction Enzyme Site Predictor (Note: the Browser also has a track with restriction sites.) -#email NEEDTOFILLOUT -maxSize 300000 -url http://nc2.neb.com/NEBcutter2/enzcut.php -param no_dam 0 -param add_type13 0 -param add_nick 0 -param sequence $seq -param no_ecobi 0 -param seqisfrag 0 -param no_ecoki 0 -param no_dcm 0 -param no_cpg 0 -param cut_to 0 -param gcode 11 -param min_orf 100 -param cut_from 0 -param circular 0 -param add_homing 0 -param enz_suppl 1 - -tool RnaFold -shortLabel RNAfold -longLabel RNA secondary structure prediction -url http://rna.tbi.univie.ac.at/cgi-bin/RNAfold.cgi -email rna@tbi.univie.ac.at -maxSize 5000 -param SHAPEFILE -param reliability on -param shape_beta 0.8 -param FILE -param EMAIL your e-mail -param SHAPEDATA -param mountain on -param Temp 37 -param shape_conv_linearlog_s 1.6 -param CONSTRAINT -param shapemethod deigan -param param rna2004 -param shape_slope 1.9 -param shape_conv_linearlog_i -2.29 -param method p -param shape_conv_linear_i 0.2 -param deigan_conversion linearlog -param dangling d2 -param SCREEN $seq -param shape_conv_linear_s 0.68 -param proceed -param svg on -param noLP on -param shape_conv_cutoff 0.25 -param shape_intercept -0.7 -param PAGE 2 - -tool rsatMeta -shortLabel RSAT Metazoa -longLabel Regulatory Sequence Analysis Tools for Metazoa. Can search for Transcription Factor binding sites and over-represented words. -url http://rsat.sb-roscoff.fr/convert-seq.cgi -email Jacques.van-Helden@univ-amu.fr -maxSize 50000 -param short_size 30 -param line_width 60 -param sequence $seq -param output_format fasta -param mask non-dna -param .cgifields addrcoutput -param .submit GO -param short_action no treatment -param sequence_format raw -param output display -param uploaded_file -param user_email - -tool promoter2 -shortLabel Promoter 2 -longLabel Vertebrate Transcription Start Site Prediction -url http://www.cbs.dtu.dk/cgi-bin/webface2.fcgi -email rapacki@cbs.dtu.dk -maxSize 50000 -param configfile /usr/opt/www/pub/CBS/services/Promoter-2.0/Promoter.cf -param SEQPASTE $seq -param SEQSUB - -## removed after request from Martha Bulyk. They plan to make their matrix search faster -#tool uniprobe -#shortLabel Uniprobe -#longLabel Search for transcription factor binding sites -#url http://the_brain.bwh.harvard.edu/uniprobe/browse.php -#email uniprobe@genetics.med.harvard.edu -#maxSize 80 -#param MAX_FILE_SIZE 2097152 -#param dnaSpeciesFormat all -#param dnaThreshold 0.45 -#param dnaSpeciesTextArea -#param dnaSpeciesSingle Acanthamoeba castellanii -#param dnaTextarea $seq -#param searchParam -#param dnaSpeciesCategory Acanthamoeba castellanii,Allomyces macrogynus,Ashbya gossypii,Arabidopsis thaliana,Aspergillus nidulans,Caenorhabditis elegans,Cryptosporidium parvum,Drosophila melanogaster,Homo sapiens,Kluyveromyces lactis,Monosiga brevicollis,Mus musculus,Mycosphaerella graminicola,Nematostella vectensis,Patiria miniata,Plasmodium falciparum,Saccharomyces cerevisiae,Strongylocentrotus purpuratus,Trichoplax adhaerens,Tuber melanosporum -#param dnaFile -#param dnaFormat textarea - tool primerBlast shortLabel Primer-BLAST longLabel Primer3-based primer designer that also checks matches via NCBI BLAST url http://www.ncbi.nlm.nih.gov/tools/primer-blast/primertool.cgi email info@ncbi.nlm.nih.gov maxSize 50000 param EXCLUDED_REGIONS param PRIMER_INTERNAL_OLIGO_MAX_GC 80.0 param LOW_COMPLEXITY_FILTER on param SELF_ANY 8.00 param SALT_FORMULAR 1 param PRIMER_INTERNAL_OLIGO_OPT_TM 60.0 param PRIMER_INTERNAL_OLIGO_MIN_SIZE 18 param PRIMER_NUM_RETURN 10 param OVERLAP_3END 4 @@ -269,72 +166,52 @@ param PRIMER_INTERNAL_OLIGO_OPT_SIZE 20 param PRIMER_LEFT_INPUT param PRODUCT_MIN_TM param PRIMER_MAX_TEMPLATE_MISPRIMING_TH 40.00 param PRIMER_MAX_TM 63.0 param PRIMER3_END param POLYX 5 param PRIMER_INTERNAL_OLIGO_MIN_GC 20.0 param NUM_OPTS_DIFFS 0 param GC_CLAMP 0 param PRIMER_MAX_DIFF_TM 3 param MAX_CANDIDATE_PRIMER 500 param CUSTOM_DB param PRIMER_PAIR_MAX_TEMPLATE_MISPRIMING 24.00 -tool crispor -url http://tefor.net/crisporMax/crispor.cgi -email services@tefor.net -shortLabel CRISPOR -longLabel CRISPR/Cas9 target selector and offtarget-predictor -param org $db -param pos $position -param pam NGG -maxSize 1000 - -tool chopchop -url https://chopchop.rc.fas.harvard.edu/search.php -email tessa.montague@gmail.com -shortLabel CHOPCHOP -longLabel CRISPR/Cas9 target selector and offtarget-predictor -maxSize 2000 -onlyDbs anoGam1,ce10,dm3,hg19,hg38,danRer7,galGal4,gasAcu1,mm10,musFur1,rn6,oryLat2,sacCer3,xenTro3 -param organism $db -param pasteSeq $seq -param position $position -param method CRISPR -param target CODING -param subsetExon -param padding -param enzyme N -param minResSite 4 -param searchMethod hsu -param 5prime GN,NG -param PAM NGG -param TALEdist -param TALEsize -param mismatches 2 -param gRVD NN -param PRODUCT_SIZE_MIN 150 -param PRODUCT_SIZE_MAX 290 -param PRIMER_MIN_SIZE 18 -param PRIMER_MAX_SIZE 25 -param PRIMER_OPT_SIZE 22 -param PRIMER_MIN_TM 57 -param PRIMER_MAX_TM 63 -param PRIMER_OPT_TM 60 -param sitePadding 20 +tool nebcutter +shortLabel NEBCutter +longLabel New England Biolabs Restriction Enzyme Site Predictor (Note: the Browser also has a track with restriction sites.) +#email NEEDTOFILLOUT +maxSize 300000 +url http://nc2.neb.com/NEBcutter2/enzcut.php +param no_dam 0 +param add_type13 0 +param add_nick 0 +param sequence $seq +param no_ecobi 0 +param seqisfrag 0 +param no_ecoki 0 +param no_dcm 0 +param no_cpg 0 +param cut_to 0 +param gcode 11 +param min_orf 100 +param cut_from 0 +param circular 0 +param add_homing 0 +param enz_suppl 1 tool regrna2 shortLabel RegRNA 2 longLabel Predicts pre-mRNA motifs, polyadenylation sites, splicing motifs, Ribosome binding sites, UTR motifs, RNA editing sites, Riboswitches, RNA regulatory elements and miRNA and ncRNA target sites email kevinchang1025@gmail.com url http://regrna2.mbc.nctu.edu.tw/detection_output.php onlyDbs hg17,hg18,hg19,hg38 maxSize 2000 param GeneSplicer_species Human param position_line_interval_len 100 param S1 $faSeq param UTRsite ON param ncRNA_FE -20 param SplicingMotif ON param Rfam ON @@ -357,15 +234,138 @@ param Polya ON param miRNA_species Homo sapiens param tfbs_species human, Homo sapiens param RNAediting ON param miRNA_FE -25 param ncRNA_species Homo_sapiens param LongStem ON param fRNAdb_match_len 30 param fRNAdb_similarity 0.9 param B1 Submit param AUrich ON param accessibility_window_size 100 param LongStem_len 40 param RiboSW ON param Size 950 + +tool RnaFold +shortLabel RNAfold +longLabel RNA secondary structure prediction +url http://rna.tbi.univie.ac.at/cgi-bin/RNAfold.cgi +email rna@tbi.univie.ac.at +maxSize 5000 +param SHAPEFILE +param reliability on +param shape_beta 0.8 +param FILE +param EMAIL your e-mail +param SHAPEDATA +param mountain on +param Temp 37 +param shape_conv_linearlog_s 1.6 +param CONSTRAINT +param shapemethod deigan +param param rna2004 +param shape_slope 1.9 +param shape_conv_linearlog_i -2.29 +param method p +param shape_conv_linear_i 0.2 +param deigan_conversion linearlog +param dangling d2 +param SCREEN $seq +param shape_conv_linear_s 0.68 +param proceed +param svg on +param noLP on +param shape_conv_cutoff 0.25 +param shape_intercept -0.7 +param PAGE 2 + +tool promoter2 +shortLabel Promoter 2 +longLabel Vertebrate Transcription Start Site Prediction +url http://www.cbs.dtu.dk/cgi-bin/webface2.fcgi +email rapacki@cbs.dtu.dk +maxSize 50000 +param configfile /usr/opt/www/pub/CBS/services/Promoter-2.0/Promoter.cf +param SEQPASTE $seq +param SEQSUB + +tool rsatMeta +shortLabel RSAT Metazoa +longLabel Regulatory Sequence Analysis Tools for Metazoa. Can search for Transcription Factor binding sites and over-represented words. +url http://rsat.sb-roscoff.fr/convert-seq.cgi +email Jacques.van-Helden@univ-amu.fr +maxSize 50000 +param short_size 30 +param line_width 60 +param sequence $seq +param output_format fasta +param mask non-dna +param .cgifields addrcoutput +param .submit GO +param short_action no treatment +param sequence_format raw +param output display +param uploaded_file +param user_email + +## removed after request from Martha Bulyk. They plan to make their matrix search faster +#tool uniprobe +#shortLabel Uniprobe +#longLabel Search for transcription factor binding sites +#url http://the_brain.bwh.harvard.edu/uniprobe/browse.php +#email uniprobe@genetics.med.harvard.edu +#maxSize 80 +#param MAX_FILE_SIZE 2097152 +#param dnaSpeciesFormat all +#param dnaThreshold 0.45 +#param dnaSpeciesTextArea +#param dnaSpeciesSingle Acanthamoeba castellanii +#param dnaTextarea $seq +#param searchParam +#param dnaSpeciesCategory Acanthamoeba castellanii,Allomyces macrogynus,Ashbya gossypii,Arabidopsis thaliana,Aspergillus nidulans,Caenorhabditis elegans,Cryptosporidium parvum,Drosophila melanogaster,Homo sapiens,Kluyveromyces lactis,Monosiga brevicollis,Mus musculus,Mycosphaerella graminicola,Nematostella vectensis,Patiria miniata,Plasmodium falciparum,Saccharomyces cerevisiae,Strongylocentrotus purpuratus,Trichoplax adhaerens,Tuber melanosporum +#param dnaFile +#param dnaFormat textarea + +tool crispor +url http://tefor.net/crisporMax/crispor.cgi +email services@tefor.net +shortLabel CRISPOR +longLabel CRISPR/Cas9 target selector and offtarget-predictor +param org $db +param pos $position +param pam NGG +maxSize 1000 + +tool chopchop +url https://chopchop.rc.fas.harvard.edu/search.php +email tessa.montague@gmail.com +shortLabel CHOPCHOP +longLabel CRISPR/Cas9 target selector and offtarget-predictor +maxSize 2000 +onlyDbs anoGam1,ce10,dm3,hg19,hg38,danRer7,galGal4,gasAcu1,mm10,musFur1,rn6,oryLat2,sacCer3,xenTro3 +param organism $db +param pasteSeq $seq +param position $position +param method CRISPR +param target CODING +param subsetExon +param padding +param enzyme N +param minResSite 4 +param searchMethod hsu +param 5prime GN,NG +param PAM NGG +param TALEdist +param TALEsize +param mismatches 2 +param gRVD NN +param PRODUCT_SIZE_MIN 150 +param PRODUCT_SIZE_MAX 290 +param PRIMER_MIN_SIZE 18 +param PRIMER_MAX_SIZE 25 +param PRIMER_OPT_SIZE 22 +param PRIMER_MIN_TM 57 +param PRIMER_MAX_TM 63 +param PRIMER_OPT_TM 60 +param sitePadding 20