FORMATDB ARGUMENTS

Sep 30, 14
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  • www.bios.niu.edu/johns/bioinform/blast_info.htm‎CachedSimilarThe official formatdb README file. A useful guide to formatdb at NCBI . The
  • It's generally not necessary to adjust this parameter. formatdb Parameters
  • mootools.net/docs/more/Types/Date‎CachedSimilarTwo Arguments (property, value) . One Argument (properties) . . new Date().
  • darwin.informatics.indiana.edu/yonli/I519Fall09/. /formatdb.htm‎Cachedformatdb 2.2.21 arguments: -t Title for database file [String] Optional -i Input file(s)
  • https://wiki.ices.utexas.edu/clsb/browser/trunk/. /formatdb.html?. ‎Cached64, The formatdb options are summarized below: 65. 66, formatdb 2.2.11
  • www.korilog.com/attachments/kdms_user_guide_en.pdf‎CachedKorilog Databank Manager System extended formatdb conversion . . . In the
  • etutorials.org/Misc/blast/Part. /13.4+formatdb+Parameters/‎CachedSimilarformatdb turns FASTA files into BLAST databases (ASN.1 format is also
  • www.ncbi.nlm.nih.gov/IEB/ToolBox/C_DOC/lxr/. /formatdb.html‎CachedSimilarOnce a source database file has been formatted by formatdb it 49 is not . 63 64
  • www.cbrg.ox.ac.uk/analysis_tools/BLAST/formatdb.shtml‎CachedSimilarMar 9, 2007 . This file is then used to construct the index for the BLAST database using a
  • emboss.sourceforge.net/apps/release/6.0/emboss/. /dbiblast.html‎Cached. (blast1 from pressdb or setdb, and blast2 from formatdb) with different index file
  • pbil.univ-lyon1.fr/BLAST/description.html‎CachedSimilarMay 25, 1998 . formatdb arguments: -t Title for database file [String] Optional -i Input file for
  • www.mathworks.com/help/bioinfo/ref/blastformat.html‎CachedSimilarspecifies options using the input arguments for the NCBI formatdb function.
  • wiki.christophchamp.com/index.php/Formatdb‎CachedJul 24, 2008 . formatdb 2.2.5 arguments: -t Title for database file [String] Optional -i Input file(s)
  • https://groups.google.com/d/topic/blast2go/PGk00XesZV8‎CachedSimilari) How to create our own db files using "formatdb" command from fasta files of .
  • https://github.com/biocore/brokit/blob/master/brokit/formatdb.py‎Cachedclass FormatDb(CommandLineApplication): """ ApplicationController for
  • The '-o' parameter, when set to 'T', causes formatdb to create indices that allow
  • pycogent.org/cookbook/blast.html‎CachedSimilarblastall 2.2.22 arguments: -p Program Name [String] -d Database [String] default
  • https://www.biostars.org/p/10414/‎CachedError: (106.18) NCBI C++ Exception: Error: (CArgException::eSynopsis) Too
  • www.bio.davidson.edu/courses/genomics/2008/. /LocalBlast.html‎CachedSimilarbin/formatdb - We will need to specify 3 arguments when running formatbd: -i, -p,
  • https://wiki.gacrc.uga.edu/wiki/Mpiblast‎CachedSimilarMar 27, 2013 . Category. Bioinformatics. Program On. zcluster. Version. 1.6.0. Author /
  • qiime.org/scripts/exclude_seqs_by_blast.html‎CachedSimilarInput Arguments: Note . -no_clean: If set, don't delete files generated by
  • signal.biosi.cf.ac.uk/cgi-bin/emboss/help/dbiblast‎CachedYou must create the old style of Blast indices by adding -A F to the formatdb
  • pic.dhe.ibm.com/. /c_cdm_ig_encryption_master_and_data_keys.html‎CachedSimilarArguments. The following list illustrates the argument semantics: /GMK: Flag for
  • www3.imperial.ac.uk/pls/portallive/docs/1/5037998.RPS‎CachedSimilar-H get help (overrides all other arguments) Note: It is not enforced that the values
  • www.bio.ku.dk/nuf/resources/BLAST_index.htm‎CachedSimilarShow a list of all arguments. . \formatdb -i Cad16_aa.fasta -p T -o F . About the
  • seqanswers.com/forums/archive/index.php/t-6117.html‎CachedSimilarI am not sure what parameter I should use (for standalone BLAST) to . Did you
  • www.biostat.jhsph.edu/~jpelsis/?User_Manual. FORMATDB.PL‎CachedFORMATDB.PL . This is a wrapper script around the formatdb program provided
  • 141.80.164.19/bioinf_dokus/blastall/README_db.htm‎CachedSimilarThe formatdb options are summarized below: formatdb arguments: -t Title for
  • eu-itn-ariadne.eu/SS-II_Program.pdf‎CachedSimilarFormatdb. This formats a FASTA file of protein or nucleotide sequences to create
  • bioinf.uni-greifswald.de/bioinf/bioinfprakt11/bioperl/bioperl.html‎Cachedformatdb 2.2.21 arguments: -t Title for database file [String] Optional -i Input file(s)
  • lists.mpiblast.org/pipermail/users_lists.mpiblast.org/. /000193.html‎CachedJul 21, 2005 . The output of formatdb.log might also be useful. can you run . Check formatdb.
  • www.premierbiosoft.com/support/faq/Format_db_Files.html‎CachedFormatdb Arguments. -t Title for database file [String] Optional. -i Input file for
  • www.lcg.unam.mx/~lcollado/B/lectures/last/last.pdf‎CachedSimilarformatdb. Main arguments: ▻ -i: the input file. ▻ -p: the type of database. Use T
  • https://www.cbil.upenn.edu/svn/apidb/. /orthomcl_module.pm‎CachedSimilarOne or Two arguments: # 1. . . FormatDB\n"); write_log(" Native FormatDB
  • ergatis.diagcomputing.org/cgi/documentation.cgi?article. creation‎CachedWhen you build a component you define each how each command accepts
  • www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/9430.html‎CachedMay 22, 2007 . The key is the -o T option which tells formatdb to build the index files . I usually
  • https://www.rosettacommons.org/manuals/. /file_fragments.html‎CachedSimilartcsh% pfilt nr.fasta > filtnr tcsh% formatdb -t filtnr -i filtnr tcsh% cp filtnr.p?? $
  • www.mothur.org/wiki/Chimera.slayer‎CachedSimilarFeb 11, 2014 . You will need to have a copy of the megablast and formatdb executables in .
  • https://www.sharcnet.ca/help/index.php/MPIBLAST‎CachedSimilarAug 20, 2014 . [roberpj@orc-login1:/opt/sharcnet/mpiblast/1.6.0/bin] ./mpiformatdb --help
  • www.genebee.msu.su/blast/newblast.html‎CachedSimilarDec 18, 1998 . formatdb arguments: -t Title for database file [String] Optional -i Input file for
  • www.haktansuren.com/blast-formatdb/Oct 3, 2012 . This function helps to create your own searchable (blastable) blast database from
  • gel.ahabs.wisc.edu/mpiblast/apidocs/mpiformatdb_8cpp-source.html‎CachedSimilar00066 * Since the hacked formatdb always adds the next sequence to 00067 *
  • lipm-bioinfo.toulouse.inra.fr/download/. /README.formatdb‎CachedAlthough the FASTA format is most often used as input to formatdb, the use of .
  • www.databaseskill.com/3257263/‎CachedIs still getting bigger and previous formatdb difference,. With makeblastdb access
  • https://bugs.debian.org/144785‎CachedPackage: blast2 Version: 6.1.20011220a-2 Severity: wishlist formatdb should
  • sydney.edu.au/engineering/it/~roehm/projects/. /ncbi/formatdb.c‎Cachedi></b> <a name=L16 href="source/demo/formatdb.c#L16">16</a> <b><i></i></b
  • dendrome.ucdavis.edu/help/faq/?faq_id=4‎CachedSimilarFor nucleotide databases, ie. formatdb -i custom.faa -p F, the file extensions are .
  • www.woolfit.net/perl/51blastall.html‎CachedSimilarFormatdb is a program that comes with the standalone BLAST, that takes a fasta
  • Table 3.2 formatdb arguments Function Option -i -p Input file for formatting Type
  • faculty.cs.byu.edu/~clement/blast/doc/formatrpsdb.html‎CachedJul 23, 2004 . Formatrpsdb is designed to perform the work of formatdb, makemat and . .

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