Formatdb
Encyclopedia
formatdb is an outdated software tool in molecular bioinformatics to format protein or nucleotide databases for BLAST
. It has been replaced by the tool makeblastdb and the NCBI "strongly encourage[s]" users to stop using formatdb.
formatdb must be used in order to format protein or nucleotide source databases before these databases can be searched by BLAST
. The source database may be in either FASTA
or ASN.1 format. Although the FASTA format is most often used as input to formatdb, the use of ASN.1 is advantageous for those who are using ASN.1 as the common source for other formats such as the GenBank
report.
The opposite of operation of formatdb, extracting sequences from a blast formatted database, can be achieved by using the fastacmd program, which comes in the same package.
In the BLAST+ version, formatdb has been succeeded by makeblastdb.
BLAST
In bioinformatics, Basic Local Alignment Search Tool, or BLAST, is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences...
. It has been replaced by the tool makeblastdb and the NCBI "strongly encourage[s]" users to stop using formatdb.
formatdb must be used in order to format protein or nucleotide source databases before these databases can be searched by BLAST
BLAST
In bioinformatics, Basic Local Alignment Search Tool, or BLAST, is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences...
. The source database may be in either FASTA
FASTA
FASTA is a DNA and protein sequence alignment software package first described by David J. Lipman and William R. Pearson in 1985. Its legacy is the FASTA format which is now ubiquitous in bioinformatics.- History :...
or ASN.1 format. Although the FASTA format is most often used as input to formatdb, the use of ASN.1 is advantageous for those who are using ASN.1 as the common source for other formats such as the GenBank
GenBank
The GenBank sequence database is an open access, annotated collection of all publicly available nucleotide sequences and their protein translations. This database is produced and maintained by the National Center for Biotechnology Information as part of the International Nucleotide Sequence...
report.
The opposite of operation of formatdb, extracting sequences from a blast formatted database, can be achieved by using the fastacmd program, which comes in the same package.
In the BLAST+ version, formatdb has been succeeded by makeblastdb.
External links
- NCBI BLAST Database Format — a description of the BLAST database format with a sample program to dump the contents of the database.