fastacmd retrieves FASTA formatted sequences from a blast database that was indexed using formatdb and formatted using the '-o' option.
An example fastacmd call would be:
/biolo/ncbi/bin/fastacmd -s UniRef90_P01892 -d /blast/uniref90
fastacmd is one of the programs distributed along with the old blastall program by the NCBI. The NCBI recommends that people start using the programs of the blast+ package instead. Having said that, most documentation currently available still refers to blastall and the programs distributed with it.
http://nebc.nox.ac.uk/bioinformatics/docs/fastacmd.html
Showing posts with label bioinfo. Show all posts
Showing posts with label bioinfo. Show all posts
BioJava
Summary: BioJava is a mature open-source project that provides a framework for processing of biological data. BioJava contains powerful analysis and statistical routines, tools for parsing common file formats and packages for manipulating sequences and 3D structures. It enables rapid bioinformatics application development in the Java programming language.
Availability: BioJava is an open-source project distributed under the Lesser GPL (LGPL). BioJava can be downloaded from the BioJava website (http://www.biojava.org). BioJava requires Java 1.5 or higher.
Availability: BioJava is an open-source project distributed under the Lesser GPL (LGPL). BioJava can be downloaded from the BioJava website (http://www.biojava.org). BioJava requires Java 1.5 or higher.
bioDBnet
biological DataBase network is an application integrating a vast number of biological databases including Gene, UniProt, Ensembl, GO, Affy, RefSeq etc. The databases are created by downloading data from various public resources. They are formatted and maintained in a relational structure at the Advanced Biomedical Computing Center (ABCC).
http://biodbnet.abcc.ncifcrf.gov/
http://biodbnet.abcc.ncifcrf.gov/
Download Free Biology Books
http://freebiologybooks.blogspot.com/
http://bioinfobooks.blogspot.com/
http://www.taringa.net/posts/ebooks-tutoriales/1519038/Todo-para-el-medico-%28libros-en-ingles%29-PARTE-I.html
http://bioinfobooks.blogspot.com/
http://www.taringa.net/posts/ebooks-tutoriales/1519038/Todo-para-el-medico-%28libros-en-ingles%29-PARTE-I.html
Beginning Perl for Bioinformatics
http://oreilly.com/catalog/9780596000806/
http://www.fishgenome.org/tutorial/Beginning%20Perl%20for%20Bioinformatics/contents.html
http://www.osc.edu/supercomputing/training/bioperl/perl_bioinf_0502_part2_pdf.pdf
http://uwf.edu/msutton/bsc4434/book-examples/
http://lbbma.univ-angers.fr/education/info/exemples/
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