matlab调取ncbi数据,Read data from NCBI BLAST report file

Get a sequence from the Protein Data Bank and create a MATLAB structure.

S = getpdb('1CIV');

Use the structure as input for the BLAST search with a significance threshold of 1e-10. The first output is the request ID, and the second output is the estimated time (in minutes) until the search is completed.

[RID1,ROTE] = blastncbi(S,'blastp','expect',1e-10);

Get the search results from the report. You can save the XML-formatted report to a file for an offline access. Use ROTE as the wait time to retrieve the results.

report1 = getblast(RID1,'WaitTime',ROTE,'ToFile','1CIV_report.xml')

Blast results are not available yet. Please wait ...

report1 =

struct with fields:

RID: 'R49TJMCF014'

Algorithm: 'BLASTP 2.6.1+'

Database: 'nr'

QueryID: 'Query_224139'

QueryDefinition: 'unnamed protein product'

Hits: [1×100 struct]

Parameters: [1×1 struct]

Statistics: [1×1 struct]

Use blastread to read BLAST data from the XML-formatted BLAST report file.

blastdata = blastread('1CIV_report.xml')

blastdata =

struct with fields:

RID: ''

Algorithm: 'BLASTP 2.6.1+'

Database: 'nr'

QueryID: 'Query_224139'

QueryDefinition: 'unnamed protein product'

Hits: [1×100 struct]

Parameters: [1×1 struct]

Statistics: [1×1 struct]

Alternatively, run the BLAST search with an NCBI accession number.

RID2 = blastncbi('AAA59174','blastp','expect',1e-10)

RID2 =

'R49WAPMH014'

Get the search results from the report.

report2 = getblast(RID2)

Blast results are not available yet. Please wait ...

report2 =

struct with fields:

RID: 'R49WAPMH014'

Algorithm: 'BLASTP 2.6.1+'

Database: 'nr'

QueryID: 'AAA59174.1'

QueryDefinition: 'insulin receptor precursor [Homo sapiens]'

Hits: [1×100 struct]

Parameters: [1×1 struct]

Statistics: [1×1 struct]