http://hi.baidu.com/lidaof/blog/item/09bf863d02e9560cbaa167de.html
blastdbcmd相当于以前的fastacmd，用来从格式化好的blast数据库中取序列 我从ncbi下载了refseq_rna的库，解压后，想看看库的信息，那么： blastdbcmd -db refseq_rna -info
Database: NCBI Transcript Reference Sequences
2,120,610 sequences; 3,361,629,869 total bases Date: Apr 27, 2010 8:31 PM Longest sequence: 101,674 bases Volumes:
/home/lidaof/db/refseq_rna 我想查询gi号为224071016的序列，那么： blastdbcmd -db refseq_rna -entry 224071016
>gi|224071016|ref|XM_002303295.1| Populus trichocarpa predicted protein, mRNA
GAGTCGCTCCACAAAGTCTTGAACAAGGAATTGAAAAATGGGCAATCTGTTATTGACATTCTTGAGATCAACAGACTGCG
GAGACAGTTACTATTCCAGTCTTACATGTGGGACAACCGCCTGGTCTATGCAGCCAGTTTAGATAACAACAGCTTCCATG
ATGGTTCAAACAGCTCAACTTCAGGACAGGAGGTGAAACCACTAGGGCCAGCTAATAGTGATAAGCTCATTGAGGAAAAT
GTTGATGCCAAGCTGCTTAAAGCCTCTAACCAGCAAGGAGGCTTTGGTAGCAACACAAACCAATGTGATGCAGTTGGTCA
AGAAATAGATGTTTGTCAAGGTCCCAGTCATGGAAAAGGAGGCCAAGCTAATCCTTTTGCTGCTATGCCTGCCCGTGATC
TATCTGACATTAAGGAATCTGGTGGAAATTTTTTTAGGACCCTTTCTGATGGACAGGATCCTGTCATGGCAAATCTATCA
GATACCCTTGATGCTGCATGGACAGGTGAGAATCAACCTGGAAGTGGGACATTTAAGGATGATAATAGTAGGCTTTCTGA
TTCAGCTATGGAAGAGTCTTCAACCACAGCTGTAGGGTTGGAGGGGGTAGGTTTGGAGGGCCATGTCGAAGACCAAGTTG
GATCCAAAGTGTGCTATTCTCCTTCACCTGCATTGTCTACCAAGGACCCTGATAACATGGAAGATTCTATGAGCTGGCTA
AGAATGCCCTTCTTGAATTTCTATCGTTCGTTCAACAATAATTGTTTAACAAGCTCTGAGAAGCTTGATAGTCTGAGGGA
GTATAACCCTGTCTATATTTCATCCTTTAGGAAGTTAAAACTCCAAGATCAGGCTAGGCTGCTTCTGCCTGTGGGTGTGA
ATGACACGGTCATTCCTGTATACGACGATGAACCCACAAGTCTTATATCTTATGCTTTAGTATCGCAAGAATATCATGCC
CAGCTAACTGATGAGGGGGAAAGAGTAAAAGAATCTGGAGAATTCAGTCCATTCTCAAGTTTATCTGATACGATGTTCCA
CTCTTTTGATGAAACAAGTTTTGATTCTTATAGAAGTTTTGGATCTACAGATGAGAGCATCTTATCCATGTCTGGATCAC
GTGGCTCTTTGATTTTGGACCCACTCTCCTACACAAAGGCTTTGCATGCCAGAGTTTCTTTTGGAGATGACAGCCCAGTT
GGTAAGGCAAGATATTCCGTGACATGCTACTATGCAAAACGGTTTGAAGCCTTAAGGAGGATATGTTGTCCATCTGAACT
TGATTATATAAGGTCTCTTAGTCGTTGTAAGAAGTGGGGAGCTCAAGGTGGCAAGAGCAATGTCTTCTTTGCAAAAACCT
TGGATGATCGCTTTATCATCAAACAAGTCACAAAAACAGAATTGGAGTCGTTTATAAAATTTGCTCCTGCTTACTTCAAG
TATCTCTCTGAGTCAATTAGCTCAAGAAGTCCAACATGCCTGGCAAAGATTTTGGGAATTTATCAGGTTACATCGAAGCT
TCTGAAAGGTGGGAAAGAAACGAAGATGGACGTTCTAGTTATGGAAAACCTTCTATTTAGGAGGAAAGTGACCCGCCTTT
ATGATCTTAAAGGATCTTCCCGGTCACGGTATAATTCGGATTCTAGTGGGAGCAACAAGGTTCTGCTGGATCAGAACTTG
ATTGAAGCAATGCCGACCTCTCCCATTTTTGTGGGAAACAAGGCAAAGCGGCTGCTGGAAAGAGCTGTCTGGAATGACAC
TTCTTTTCTTGCATCGATTGATGTAATGGATTACTCATTATTGGTTGGGGTGGATGAAGAGAAGCACGAGTTAGTACTTG
GGATAATTGATTTCATGAGGCAGTATACATGGGACAAGCATTTGGAAACATGGGTCAAGGCTTCAGGCATACTTGGCGGT
CCAAAGAATGCTTCACCAACTGTTATTTCTCCGAAGCAATATAAGAAGAGGTTCAGGAAAGCGATGACGACCTATTTTCT
GATGGTCCCAGATCAATGGTCCCCTCCCACTATCATTCTAAGTAAATCCCAATCTGATTTTGGCGAAGAGAACACACAAG
GTGCGACTTCAGTTGACTGATATTGTGGGTCCGTGTTCTTGTACATGTAAACTTGAATTTTGGGATCTTCCCACAATTTT
TCTCTCATTCTTAATTTTTCCTTTCATTTTTTATTTTTTATTTTTGTTTTATAGAAATTACTACTGTAACTTTAGTTAAG
AAGAGAAGCTTATAATTATTTGTTAGGAAATGCAGAACAAGGCTGTCATAGCCATGAGATTCGGTTGGGGGTATAATATT
GGATGACCTT 呵呵，是不是挺方便呢 加-help参数显示blastdbcmd的详细帮助哦，如下： blastdbcmd -help
USAGE
blastdbcmd [-h] [-help] [-db dbname] [-dbtype molecule_type]
[-entry sequence_identifier] [-entry_batch input_file] [-pig PIG] [-info]
[-range numbers] [-strand strand] [-mask_sequence_with numbers]
[-out output_file] [-outfmt format] [-target_only] [-get_dups]
[-line_length number] [-ctrl_a] [-version] DESCRIPTION
BLAST database client, version 2.2.23+ OPTIONAL ARGUMENTS
-h
Print USAGE and DESCRIPTION; ignore other arguments
-help
Print USAGE, DESCRIPTION and ARGUMENTS description; ignore other arguments
-version
Print version number; ignore other arguments *** BLAST database options
-db <String>
BLAST database name
Default = `nr'
-dbtype <String, `guess', `nucl', `prot'>
Molecule type stored in BLAST database
Default = `guess' *** Retrieval options
-entry <String>
Comma-delimited search string(s) of sequence identifiers:
e.g.: 555, AC147927, 'gnl|dbname|tag', or 'all' to select all
sequences in the database
* Incompatible with: entry_batch, pig, info
-entry_batch <File_In>
Input file for batch processing (Format: one entry per line)
* Incompatible with: entry, pig, info
-pig <Integer, >=0>
PIG to retrieve
* Incompatible with: entry, entry_batch, target_only, info
-info
Print BLAST database information
* Incompatible with: entry, entry_batch, outfmt, strand, target_only,
ctrl_a, get_dups, pig, range *** Sequence retrieval configuration options
-range <String>
Range of sequence to extract (Format: start-stop)
* Incompatible with: info
-strand <String, `minus', `plus'>
Strand of nucleotide sequence to extract
Default = `plus'
* Incompatible with: info
-mask_sequence_with <String>
Produce lower-case masked FASTA using the algorithm IDs specified (Format:
N,M,...) *** Output configuration options
-out <File_Out>
Output file name
Default = `-'
-outfmt <String>
Output format, where the available format specifiers are:
%f means sequence in FASTA format
%s means sequence data (without defline)
%a means accession
%g means gi
%o means ordinal id (OID)
%t means sequence title
%l means sequence length
%T means taxid
%L means common taxonomic name
%S means scientific name
%P means PIG
%mX means sequence masking data, where X is an optional comma-
separted list of integers to specify the algorithm ID(s) to
diaplay (or all masks if absent or invalid specification).
Masking data will be displayed as a series of 'N-M' values
separated by ';' or the word 'none' if none are available.
For every format except '%f', each line of output will correspond to
a sequence.
Default = `%f'
* Incompatible with: info
-target_only
Definition line should contain target GI only
* Incompatible with: pig, info, get_dups
-get_dups
Retrieve duplicate accessions
* Incompatible with: info, target_only *** Output configuration options for FASTA format
-line_length <Integer, >=1>
Line length for output
Default = `80'
-ctrl_a
Use Ctrl-A as the non-redundant defline separator
* Incompatible with: info
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