blast ftp

NCBI BLAST FTP Site

Tao Tao, Ph.D.
User Service
NCBI, NLM, NIH

TOC

1. Introduction content
2. File list and content content
3. Techinical Support

NCBI BLAST ftp site (ftp.ncbi.nlm.nih.gov) provides software packages for standalone blast, client server blast, and wwwblast packages for various platforms. It also provides commonly used blast databases in preformatted as well as FASTA format. Documents on the blast executables and other related subjects are also available from this site.

This file describes the the subdirectories and files found on this ftp site. It also prvoides the basic information on file content and on how the files should be used.

2. File list and content

This section list and describes the files found on the BLAST FTP site. File content for each directory/subdirectory is described in a separate table.

2.1 ftp.ncbi.nlm.nih.gov/blast/ general directory content

The blast ftp directory contains several subdirectories each for a specific set of files.

Table 2.1 ftp.ncbi.nlm.nih.gov/blast/ general directory content
File/Dir Name	Content
blastftp.html	README on FTP site (this file)
db	databases in preformatted or FASTA form
demo	demonstration programs and documents from blast developers
documents	documents for programs in standalone blast, netblast, and wwwblast programs
executables	archives for binary distribution of blast programs
matrices	protein and nucleotide score matrices, only a subset are supported by blast
temp	temporary directory for miscellaneous files

2.2 /blast/db/ directory content

Databases larger than two gigabytes (2 GB) are formatted in multiple volumes, which are named using the "database.##.tar.gz" convention. All relevant volumes are required. An alias file is provided so that the database can be called using the alias name without the extension (.nal or .pal). For example, to call est database, simply use "–d est" option in the commandline (without the quotes).

Certain databases are subsets of a larger parental database. For those databases, mask files, rather than actual databases, are provided. The mask file needs the parent database to function properly. The parent databases should be generated on the same day as the mask file. For example, to use swissprot preformatted database, swissprot.tar.gz, one will need to get the nr.tar.gz with the same date stamp.

To use the preformatted blast database file, first inflate the file using gzip (unix, linux), WinZip (window), or StuffIt Expander (Mac), then extract the component files out from the resulting tar file using tar (unix, linux), WinZip (Window), or StuffIt Expander (Mac). The resulting files are ready for BLAST.

Table 2.2 /blast/db/ directory content
File/Dir Name	Content
FASTA	subdirectory with databases in FASTA format
blastdb.html	content list of the blast databases
est.*.tar.gz	volumes of the est database, all are needed to reconstitute complete est database
est_human.tar.gz	human est database, a mask file requires all volumes of est to work
est_mouse.tar.gz	mouse est database, a mask file requires all volumes of est to work
est_others.tar.gz	non-human, non-mouse est database, a mask file reqires both volumes of est
gss.*.tar.gz	genomic survery sequence database, all are needed to reconstitute complete gss database
htgs.*.tar.gz	volumes of the htgs database, all are needed to reconstitute complete htgs database
human_genomic.tar.gz	human chromosome database containing concatenated contigs with adjusted gaps represented by N's
nr.*.tar.gz	volumes of non-redundant protein database, all are needed to reconstitute complete nr
nt.*.tar.gz	volumes of the nucleotide "nr" database, all are needed to reconstitute complete nt database
other_genomic.*.tar.gz	volumes of chromosome database for organisms other than human, all are needed to reconstitute complete other_genomic database
pataa.tar.gz	patent protein database
patnt.tar.gz	patent nucleotide database
pdbaa.tar.gz	protein sequence database from pdb entries, a mask file requires all nr.*.tar.gz to function
pdbnt.tar.gz	nucleotide sequence database from pdb entries. They are not the coding sequences for the corresponding protein structure entries!
sts.tar.gz	sequence tag site database
swissprot.tar.gz	swissprot sequence database, last major release. It requires all nr.*.tar.gz to work properly
taxdb.tar.gz	taxonomy id database for use with the above file to retrieve taxonomic information for specific entries
wgs.*.tar.gz	volumes of wgs assembly database, all volumes are needed to reconsititute wgs database

2.2.1 /blast/db/FASTA/ subdirectory content

The FASTA database files are now stored in this subdirectory, it does contain some additional databases that are not available via the NCBI BLAST pages. Due to file size issues, the full est database is not provided. One needs to get the three subsets and concatenate them together to get the complete est database.

These databases will need to be formatted using formatdb program found in the standalone blast executable package. The recommended commandlines to use are:

formatdb –i input_db –p F –o T for nucleotide
formatdb –i input_db –p T –o T for protein

For additional information on formatdb, please see the formatdb.html at:

/blast/documents/formatdb.html

2.2.1 blast/db/FASTA/ subdirectory content
File/Dir Name	Content
alu.a.gz	proteins translated from alu.n
alu.n.gz	alu repeat sequences
drosoph.aa.gz	Drosophila protein from genome annotation
drosoph.nt.gz	Drosophila genome
ecoli.aa.gz	E.coli K-12 proteins from genome annotation
ecoli.nt.gz	E.coli K-12 genomic contigs
est_human.gz	human subset of the est database
est_mouse.gz	mouse subset of the est database
est_others.gz	subset of est other than human or mouse entries
gss.gz	Genomic Survey Sequences (mostly BAC ends)
htgs.gz	High Throughput Genomic Sequences
human_genomic.gz	Human chromosomes formed by concatenating genomic contig assemblies (NT_######) and adjusting the gaps with N’s
igSeqNt.gz	Immunoglobulin nucleotide sequences
igSeqProt.gz	Immunoglobulin protein sequences
mito.aa.gz	protein from the annotated mitochondrial genomes
mito.nt.gz	mitochondrial genomes
month.aa.gz	protein sequences released or updated in the past 30 days
month.est_human.gz	human subset of EST released/updated in the past 30 days
month.est_mouse.gz	mosue subset of EST released/updated in the past 30 days
month.est_others.gz	non-human non-mouse EST, released or updated in the past 30 days
month.gss.gz	gss entries released/updated in the past 30 days
month.htgs.gz	htgs entries released/updated in the past 30 days
month.nt.gz	subset of nt released/updated in the past 30 days
nr.gz	non-redundant protein sequence database
nt.gz	nucleotide database from GenBank excluding the batch division htgs, est, gss,sts, pat divisions, and wgs entries. Not non-redundant
other_genomic.gz	Chromosome entries other than human
pataa.gz	Patent protein sequence database
patnt.gz	Patent nucleotide sequence database
pdbaa.gz	protein sequences for pdb entries
pdbnt.gz	nucleotide entries for pdb entries. They are NOT the coding sequence forthe corresponding protein entries
sts.gz	Sequence Tag Sites database
swissprot.gz	swissprot database, last major release
vector.gz	vector sequences from synthetic (syn) division of GenBank
wgs.gz	Whole Genome Shotgun sequence assembly
yeast.aa.gz	protein translations from yeast genome annotation
yeast.nt.gz	yeast genomic sequence

2.3 File content for /blast/demo/ directory

This directory contains some technical presentt-family: co gb|accession|locus EMBL Data Library emb|accession|locus DDBJ, DNA Database of Japan dbj|accession|locus NBRF PIR pir||entry Protein Research Foundation prf||name SWISS-PROT sp|accession|entry name Brookhaven Protein Data Bank pdb|entry|chain Patents pat|country|number GenInfo Backbone Id bbs|number General database identifier gnl|database|identifier NCBI Reference Sequence ref|accession|locus Local Sequence identifier lcl|identifier "gi" identifiers are being assigned by NCBI for all sequences contained within NCBI's sequence databases. The "gi" identifier provides a uniform and stable naming convention whereby a specific sequence is assigned its unique gi identifier. If a nucleotide or protein sequence changes, however, a new gi identifier is assigned, even if the accession number of the record remains unchanged. Thus gi identifiers provide a mechanism for identifying the exact sequence that was used or retrieved in a given search. We recommend that "gi display option" be activated in local blast search by setting the -I option to T, which was set to false by default: -I Show GI's in deflines [T/F] default = F For databases whose entries are not from official NCBI sequence databases, such as Trace database, the gnl| convention is used. For custom database, this convention should be followed and the id for each sequence must be unique, if one would like to take the advantage of indexed database, which enables specific sequence retrieval using fastacmd program included in the blast executable package. One should refer to documents distributed in the standalone BLAST package for more details. 6. Formatting the FASTA database FASTA database files need to be formatted with formatdb before they can be used in local blast search. For those from NCBI, the following formatdb are recommended: formatdb -i input_db -p F -o T for nucleotide formatdb -i input_db -p T -o T for protein The -A option introduced in 2.2.3 is now built into the formatdb program and thus removed from the list of configurable options since 2.2.8. This enables formatdb to properly handle large sequence files (longer than 16 million bases). Please refer to formatdb.html under the /blast/documents directory for more information. Databases prepared using 2.2.8 formatdb will not be backward compatible with blast programs old than version 2.2.3. 7. Technical Support Questions and comments on this document and NCBI BLAST related questions should be sent to blast-help group at: blast-help@ncbi.nlm.nih.gov For information about other NCBI resources/services, please send email to NCBI User Service at: info@ncbi.nlm.nih.gov $Header: /src/NCBI/vault.ncbi/distrib/doc/blast/blastdb.html,v 1.10 2008/10/02 16:01:03 camacho Exp $ ./usr/share/doc/blast2/blastftp.html0000644000000000000000000006170210401610760016266 0ustar rootroot blast ftp