d8aef11766e1720af30e848211b03a1bee002cf7 max Fri Aug 21 03:14:29 2015 -0700 adding chopchop and nebcutter and fixing an obvious bug. Also adding a little tool that parse a Chrome HTTP trace and creates the extTools.ra entry mostly automatically. refs #15113 diff --git src/hg/hgTracks/extTools.ra src/hg/hgTracks/extTools.ra index 98f155d..7d02342 100644 --- src/hg/hgTracks/extTools.ra +++ src/hg/hgTracks/extTools.ra @@ -65,30 +65,53 @@ 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 @@ -127,46 +150,47 @@ 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 -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 +## 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 @@ -255,15 +279,46 @@ 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 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