Structure Prediction      Fragment Libraries      Alanine Scanning
[ Queue ] [ Submit ]      [ Queue ] [ Submit ]      [ Queue ] [ Submit ]
[ Register / Update ] [ Docs / FAQs ]


      If you have questions or comments, feel free to contact me at DCChivian-at-lbl.gov


Download dylanUtil


Dylan's Utilities Download CONTENTS 

src/msaUtil:
total 200
-r-xr-xr-x  1 dylan dylan 13888 Aug  7  2004 addTermini2msa.pl
-rwxr-xr-x  1 dylan dylan   263 Jan  7  2004 asciifyBlastCheckfile.sh
-r-xr-xr-x  1 dylan dylan 41019 Aug  7  2004 blast2msa.pl
-rwxr-xr-x  1 dylan dylan  1753 Jan  7  2004 blosum62.qij
-r-xr-xr-x  1 dylan dylan  6299 Aug  7  2004 cleanCheck.pl
-r-xr-xr-x  1 dylan dylan  5629 Aug  7  2004 fasta_dbm_create.pl
-r-xr-xr-x  1 dylan dylan 12572 Aug  7  2004 getPsiBlastPdbHits.pl
-r-xr-xr-x  1 dylan dylan  7330 Aug  7  2004 msa2msf.pl
-r-xr-xr-x  1 dylan dylan 22899 Aug  7  2004 msa2profile.pl
-r-xr-xr-x  1 dylan dylan  7601 May  1  2005 pdb_blast.pl
-r-xr-xr-x  1 dylan dylan 12986 Aug  7  2004 quickblast.pl
-rwxr-xr-x  1 dylan dylan 13745 Jan  7  2004 readblastmatrix
-r-xr-xr-x  1 dylan dylan  5806 Aug  7  2004 updateNR.pl
-r-xr-xr-x  1 dylan dylan 10431 Oct  3  2004 updatePdbDerivedData.pl
-r-xr-xr-x  1 dylan dylan  6808 Aug  7  2004 updateSeqresAndSSdbs.pl

src/mstraUtil:
total 260
-r-xr-xr-x  1 dylan dylan 12129 Aug  7  2004 get3dpair.pl
-r-xr-xr-x  1 dylan dylan 11566 Aug  7  2004 get3dpairQuickCA.pl
-r-xr-xr-x  1 dylan dylan 63940 Aug  7  2004 getStradStack.pl
-r-xr-x---  1 dylan dylan 62696 May  5  2005 getTaylorParseConsensus.pl
-r-xr-xr-x  1 dylan dylan 13118 Aug  7  2004 stradStack2fitpdbs.pl
-r-xr-xr-x  1 dylan dylan 45145 Aug  7  2004 stradStack2profile.pl
-r-xr-x---  1 dylan dylan 16123 May  5  2005 taylorBlast.pl
-r-xr-x---  1 dylan dylan 19694 Apr 30  2005 taylorParse.pl

src/pdbUtil:
total 724
-r-xr-xr-x  1 dylan dylan 14281 Aug  7  2004 3dpair2zonesClean.pl
-r-xr-xr-x  1 dylan dylan 13081 Aug  7  2004 3dpair2zones.pl
-r-xr-xr-x  1 dylan dylan  2079 Aug  7  2004 addChain.pl
-r-xr-xr-x  1 dylan dylan  5761 Aug  7  2004 cleanPdbCA.pl
-r-xr-xr-x  1 dylan dylan  7755 Aug  7  2004 cleanPdb.pl
-rwxr-xr-x  1 dylan dylan  8336 Aug 12  2004 colorBfactorByZones.pl
-rwxr-xr-x  1 dylan dylan 13893 May  1  2005 completeAlignmentMap.pl
-r-xr-xr-x  1 dylan dylan 78676 May  5  2005 completePdbCoords.pl
-r-xr-xr-x  1 dylan dylan  4340 Aug  7  2004 coordContig.pl
-r-xr-xr-x  1 dylan dylan   342 Aug  7  2004 cp_decoys.pl
-rwxr-xr-x  1 dylan dylan 39794 Sep  7  2004 createTemplateIgnoreMissing.pl
-rwxr-xr-x  1 dylan dylan 48369 Oct 23 18:50 createTemplate.pl
-r-xr-xr-x  1 dylan dylan 17517 Jul 27  2004 decoys2looplib.pl
-rwxr-xr-x  1 dylan dylan 15474 Aug  1  2004 filterLoopLib.pl
-r-xr-xr-x  1 dylan dylan 13295 Aug  7  2004 frankenPdbByZones.pl
-r-xr-xr-x  1 dylan dylan 12438 Aug  7  2004 getCompleteFastaFromCoords.pl
-r-xr-xr-x  1 dylan dylan 12292 Aug  7  2004 getFastaFromCoords.pl
-r-xr-xr-x  1 dylan dylan  5315 Aug  7  2004 getFirstChain.pl
-r-xr-xr-x  1 dylan dylan  6730 Aug  7  2004 getFirstOccResNum.pl
-r-xr-xr-x  1 dylan dylan  7357 Aug  7  2004 getIdentityFromZones.pl
-rwxr-xr-x  1 dylan dylan 26316 Oct 23 21:59 getMammothMaxsubRMSD.pl
-r-xr-xr-x  1 dylan dylan 20235 Aug  7  2004 getPdb.pl
-rwxr-xr-x  1 dylan dylan   224 Aug  1  2004 grab_atom_type.pl
-rwxr-xr-x  1 dylan dylan  5694 May  1  2005 moveMissingDensity.pl
-rwxr-xr-x  1 dylan dylan 27404 Nov 18  2004 pdb2csts.pl
-r--r--r--  1 dylan dylan  1267 Jan  7  2004 PDBFORMAT.TXT
-r-xr-xr-x  1 dylan dylan 15655 Aug  7  2004 profit_discard_zones.pl
-r-xr-xr-x  1 dylan dylan  6026 Aug  7  2004 profit_rms_zones.pl
-rwxr-xr-x  1 dylan dylan 13328 Jul 28  2004 purgeLongLoopsFromLib.pl
-rwxr-xr-x  1 dylan dylan 13327 Jul 28  2004 purgeShortLoopsFromLib.pl
-r-xr-xr-x  1 dylan dylan  5212 Aug  7  2004 removeChain.pl
-rwxr-xr-x  1 dylan dylan  9149 Aug 16  2004 removeExtendedChain.pl
-rwxr-xr-x  1 dylan dylan 20793 Aug  1  2004 removeIllegalNonHeavyAtoms.pl
-rwxrwxr-x  1 dylan dylan 13551 Sep 22  2004 removeMissingDensity
-rw-r--r--  1 dylan dylan  5468 Sep 23  2004 removeMissingDensity.c
-rwxr-xr-x  1 dylan dylan  8828 May  1  2005 removeMissingDensity.pl
-r-xr-xr-x  1 dylan dylan  6033 Aug  7  2004 removeTERs.pl
-rwxr-xr-x  1 dylan dylan 14049 Jul 14  2004 restoreLongLoopsToLib.pl
-rwxr-xr-x  1 dylan dylan 23221 Aug  2  2004 restoreMissingDensity.pl
-rwxr-xr-x  1 dylan dylan 14261 Jul 21  2004 restoreShortLoopsToLib.pl
-rwxr-xr-x  1 dylan dylan 11202 Sep  9  2004 shiftZones.pl
-r-xr-xr-x  1 dylan dylan  8065 Aug  7  2004 sliceFasta.pl
-r-xr-xr-x  1 dylan dylan  5881 Aug  7  2004 slicePdbByZones.pl
-r-xr-xr-x  1 dylan dylan  6572 Aug  7  2004 slicePdb.pl
-r-xr-xr-x  1 dylan dylan  8054 Aug  7  2004 sliceSSA.pl
-r-xr-x---  1 dylan dylan  5475 May 23  2005 stripMissingDensity.pl
-rwxr-xr-x  1 dylan dylan  6448 Aug  2  2004 zeroExtendedChain.pl
lrwxrwxrwx  1 dylan dylan    24 Mar  7 16:37 zone_len.pl -> ../zonesUtil/zone_len.pl
lrwxrwxrwx  1 dylan dylan    25 Mar  7 16:37 zones2len.pl -> ../zonesUtil/zones2len.pl
lrwxrwxrwx  1 dylan dylan    35 Mar  7 16:37 zones2selectregions.pl -> ../zonesUtil/zones2selectregions.pl

src/ssUtil:
total 100
-r-xr-xr-x  1 dylan dylan  6766 Aug  7  2004 fake_template_pred_from_ssa.pl
-r-xr-xr-x  1 dylan dylan  8865 Aug  7  2004 fake_template_pred.pl
-r-xr-xr-x  1 dylan dylan  6670 Aug  7  2004 getDsspSS.pl
-r-xr-xr-x  1 dylan dylan  3810 Aug  7  2004 getJufo.pl
-r-xr-xr-x  1 dylan dylan 12834 Aug  7  2004 getMammothSS.pl
-r-xr-xr-x  1 dylan dylan  3675 Aug  7  2004 getPsipred.pl
-r-xr-xr-x  1 dylan dylan  6368 Aug  7  2004 getSam.pl
-r-xr-xr-x  1 dylan dylan  4839 Aug  7  2004 getSSA.pl
-r-xr-xr-x  1 dylan dylan 12783 Aug  7  2004 getSSfromStruct.pl
-r-xr-xr-x  1 dylan dylan  6357 Aug  7  2004 getSS.pl
-r-xr-xr-x  1 dylan dylan  5419 Aug  7  2004 sspred_columnize.pl

src/zonesUtil:
total 396
-rwxr-xr-x  1 dylan dylan 10546 Oct 23 18:55 count_alignments.pl
-rwxrwxr-x  1 dylan dylan 14181 Oct 23 19:58 get_consensus_zones
-rw-r--r--  1 dylan dylan 19288 Oct 23 19:58 get_consensus_zones.c
-rwxr-xr-x  1 dylan dylan 17731 Oct 23 15:59 getConsensusZones.pl
-rwxr-xr-x  1 dylan dylan 12648 Oct 23 17:57 get_default_plus_random_alignments.pl
-rwxr-xr-x  1 dylan dylan 12236 Oct 23 20:05 get_first_n_alignments.pl
-rwxrwxr-x  1 dylan dylan 16751 Oct 24 02:29 score_consensus_zones
-rw-r--r--  1 dylan dylan 26255 Oct 24 02:29 score_consensus_zones.c
-rwxr-xr-x  1 dylan dylan 17160 Feb 15  2005 scoreConsensusZones.pl
-rwxr-xr-x  1 dylan dylan 53372 Sep 20  2004 uniq_oblfilt_zones.pl
-rwxr-xr-x  1 dylan dylan 69273 Sep 17  2004 uniq_trim_and_oblfilt_zones.pl
-rwxr-xr-x  1 dylan dylan 40749 Oct 14  2004 uniq_trim_zones.pl
-rwxr-xr-x  1 dylan dylan 26846 Sep 21  2004 uniq_upbound_zones.pl
-rwxr-xr-x  1 dylan dylan 12787 Oct 23 15:10 uniq_zones.pl
-r-xr-xr-x  1 dylan dylan   626 Aug  7  2004 zone_len.pl
-r-xr-xr-x  1 dylan dylan  4275 Aug  7  2004 zones2len.pl
-r-xr-xr-x  1 dylan dylan  3395 Aug  7  2004 zones2selectregions.pl












Robetta is available for NON-COMMERCIAL USE ONLY at this time
[ Terms of Service ]
Copyright © 2004-2007 University of Washington