https://stamps.mbl.edu/index.php/Kostas_Konstantinidis‎CachedAug 10, 2012 . Don't forget to edit the path to blastall and formatdb to reflect the path . alignment

defindit.com/readme_files/blast_formatdb.html‎CachedSimilarMay 9, 2008 . The NCBI formatdb silently changes accession numbers if the . keywords:

https://bcrc.bio.umass.edu/courses/spring2012/micbio/. /blast‎CachedTo do this in Terminal go to the myblast/databases directory and type. For

nebc.nerc.ac.uk/bioinformatics/documentation/blast/blastdb.html‎CachedSimilarOct 2, 2008 . tar.gz | patent nucleotide sequence database | The above two databases .

software-carpentry-at-scripps-2012-11.readthedocs.org/. /blast.html‎CachedThe 'formatdb' command creates the databases . Run the formatdb command

The dots represent identical nucleotides at the locus. . directly used to set up the

rpm.pbone.net/index.php3/stat/45/idpl/4302002/. /1/. /formatdb‎CachedOct 5, 2001 . man formatdb howto config documentation configuration . NAME. formatdb -

www.mathworks.com/help/bioinfo/ref/blastformat.html‎CachedSimilarThis MATLAB function calls a local version of the NCBI formatdb executable file .

binf.gmu.edu/software/blast/formatdb.html‎CachedSimilar. Produced by Formatdb Introduction ------------ Formatdb must be used in order

selab.janelia.org/people/farrarm/blastdbfmtv4/blastdbfmt.html‎CachedSimilar. program that converts FASTA files to the binary files used by BLAST is

www.rocksclusters.org/roll-documentation/bio/5. /blast_usage.html‎CachedSimilarUsage. BLAST can be used for protein-protein comparisons or nucleotide-

https://github.com/ice91/BibPro/blob/master/blast. /formatdb.html‎CachedFormatdb must be used in order to format protein or nucleotide source.

www.oardc.ohio-state.edu/. /BlastInstruction_update07182009.ppt‎CachedSimilarsequences. The program compares nucleotide or . nucleotide/nucleotide. blastx

www.protocol-online.org/biology-forums/posts/42161.html‎CachedSimilarformatdb is a command-line program used to create BLAST databases from a

faculty.cs.byu.edu/~clement/blast/doc/formatrpsdb.html‎CachedJul 23, 2004 . Formatrpsdb is designed to perform the work of formatdb, makemat and .

https://www.biostars.org/p/1557/‎CachedI convert this database into a blastable format using formatdb, code below: .

www.clarkfrancis.com/blast/using_blast.html‎CachedSimilarI also copy, move or link the formatdb and blastall binaries into the blast directory.

www.cbrg.ox.ac.uk/analysis_tools/BLAST/formatdb.shtml‎CachedSimilarMar 9, 2007 . creating BLAST databases (formatdb) . "customBLASTdb" from a fasta file called

https://biodoc.ist.unomaha.edu/wiki/Tutorials/blast‎CachedApr 26, 2011 . formatdb and blastall programs can be installed in ubuntu and other debian . #If

seqanswers.com/forums/archive/index.php/t-6117.html‎CachedSimilarIt could be that when you've formatted the blast database you didn't set it for

The programs 'blastall' and 'megablast' are used to search the databases created

www.bio.utk.edu/fesin/. /Houston_IMC-FESIN_7-31-10.ppt‎CachedSimilarformatdb must be used in order to format protein or nucleotide source databases

gel.ahabs.wisc.edu/mpiblast/apidocs/mpiformatdb_8cpp-source.html‎CachedSimilar00066 * Since the hacked formatdb always adds the next sequence to 00067 .

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 . The

www.bio.ku.dk/nuf/resources/BLAST_index.htm‎CachedSimilarblastx, Nucleotide query > Protein database (via translated query) . About the

www.premierbiosoft.com/support/faq/Format_db_Files.html‎Cacheddefault = formatdb.log. -p Type of file. T - protein. F - nucleotide [T/F] Optional.

nebc.nox.ac.uk/bioinformatics/docs/formatdb.html‎CachedSimilarformatdb is used to index protein or nucleotide databases so that they are

en.digipedia.org/man/doc/view/formatdb.1/‎Cachedformatdb format protein or nucleotide databases for BLAST.

ugene.unipro.ru/documentation/manual/plugins/. tool. /blast.html‎CachedSimilarblastall — the old program developed and distributed by the NCBI for running

https://wiki.gacrc.uga.edu/wiki/NCBI_Blast‎CachedSimilarMay 1, 2014 . NCBI website. jump to formatdb . deflines [T/F] default = F -q Penalty for a

https://twitter.com/torstenseemann/status/346523365114249216‎CachedJun 17, 2013 . Why can't formatdb and makeblastdb just auto-detect if it's a protein or nucleotide

manpages.ubuntu.com/manpages/natty/man1/formatdb.1.html‎Cachedformatdb must be used in order to format protein or nucleotide source databases

www3.imperial.ac.uk/bioinfsupport/help/blast_searches‎CachedSimilarThe BLAST variety you wish to use, e.g. blastn for nucleotide-nucleotide

www.bios.niu.edu/johns/bioinform/blast_info.htm‎CachedSimilartblastx, query is DNA translated into protein, subject is nucleotide translated .

nullege.com/codes/search/cogent.app.formatdb.FormatDb‎Cacheddef test_call(self): """FormatDb: Calling on a nucleotide data functions as

www.ncbi.nlm.nih.gov/IEB/ToolBox/C_DOC/lxr/. /formatdb.html‎CachedSimilar. The Files Produced by Formatdb 37 38 39 40 Introduction 41 ------------ 42

wiki.christophchamp.com/index.php/Formatdb‎CachedJul 24, 2008 . Formatdb must be used in order to format protein or nucleotide source databases

pycogent.org/. /building_and_using_an_application_controller.html‎CachedSimilarWe'll look at wrapping the formatdb application from the BLAST 2.2.20 package

oreilly.com/catalog/seqanalyian/chapter/ch07.pdf‎CachedSimilarformatdb formatdb is used to format protein or nucleotide source databases

etutorials.org/Misc/blast/Part. /13.4+formatdb+Parameters/‎CachedSimilarformatdb -i protein_db formatdb -p F -i nucleotide_db zcat est*.gz | formatdb -p .

sydney.edu.au/engineering/it/~roehm/projects/dbBLAST/ncbi.html‎Cached[URL: http://www.ncbi.nlm.nih.gov/BLAST/docs/formatdb.html] . NCBI-BLAST

www.biomedcentral.com/content/. /1471. 13. /formatdb.html‎CachedName, formatdb. Description. formatdb is used to index protein or nucleotide

puneetwadhwa.blogspot.com/. /creating-and-using-custom-blast.html‎CachedSimilarOct 20, 2005 . The formatdb command has several options, and the entire readme file may be

octupus.sourceforge.net/octu_manual.html‎CachedSimilar(Note : if your formatdb and megablast are not linked, instead type in the directory

openwetware.org/wiki/Wikiomics:BLAST_tutorial‎CachedSimilarMay 4, 2011 . translated in 6 frames nucleotide query vs protein DB. >human_genomic_seq .

141.80.164.19/bioinf_dokus/blastall/README_db.htm‎CachedSimilarFormatdb must be used in order to format protein or nucleotide source databases

pbgworks.org/sites/pbgworks.org/. /04_Francis_BioInfII_0_0.pdf‎CachedThe program compares nucleotide or protein sequences to . Translated

en.wikipedia.org/wiki/Formatdb‎CachedSimilarformatdb is a discontinued software tool that was used in molecular

www.computational-genomics.net/resources/software.html‎CachedSimilarFASTA - Sequence similarity searching against nucleotide and protein databases

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