Question

Blastp - through R

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maahpishanu • 0

@maahpishanu-9664

Last seen 8.8 years ago

Hi,

I'm supposed to do reciprocal best hit using blastp for a long list of proteins for which I'm given only the UniProtKB/TrEMBL identifier. I have to find the ortholog proteins for each of the given proteins. I also have to find orthologs in a given list of species.

Previously, when I had only one Protein, I would do it through online tool in NCBI, there I can give the identifier and also limit the species. However, with more proteins in hand, this is not feasible anymore.

I downloaded Blast, but I cannot download any databases (memory problem, and I need refseq_protein database).

I'm familiar with R and would like to do it in R, but sending online queries to the NCBI blastp.

I searched a lot and was not able to find hint.

I installed orthologr, biomaRt and some other packages, but they only used local databases.

I would appreciate it a lot if somebody could help me how I can send online query through R. I have an R code and somewhere in the code I need to call blastp to find orthologs of my proteins among the given list of species.

Thanks and looking forward.

Maah

blast R • 6.1k views

ADD COMMENT • link 8.8 years ago maahpishanu • 0

score 0 · Answer 1 · 2016-02-05

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Martin Morgan 25k

@martin-morgan-1513

Last seen 3 months ago

United States

blastSequences in the annotate package might be a partial solution. For some protein sequence query,

library(annotate)
res = blastSequences(query, "nr", program="blastp", as="XML")

The return value is XML, and would need to be processed using xpath syntax. For instance, with

> query
[1] "QIKDLLVSSSTDLDTTLVLVNAIYFKGMWKTAFNAEDTREMPFHVTKQESKPVQMMCMNNSFNVATLPAEKMKILELPFASGDLSMLVLLPDEVSDLERIEKTINFEKLTEWTNPNTMEKRRVKVYLPQMKIEEKYNLTSVLMALGMTDLFIPSANLTGISSAESLKISQAVHGAFMELSEDGIEMAGSTGVIEDIKHSPESEQFRADHPFLFLIKHNPTNTIVYFGRYWSP"

we have

> sapply(res["//Hit_id"], xmlValue)
 [1] "gi|129295|sp|P01013.1|OVALX_CHICK" "gi|448824824|ref|NP_001263315.1|" 
 [3] "gi|971382511|ref|XP_015137661.1|"  "gi|971382509|ref|XP_015137660.1|" 
 [5] "gi|971382507|ref|XP_015137659.1|"  "gi|733881413|ref|XP_010706721.1|" 
 [7] "gi|385145541|dbj|BAM13279.1|"      "gi|71897377|ref|NP_001026172.1|"  
 [9] "gi|733881415|ref|XP_010706722.1|"  "gi|971382505|ref|XP_015137657.1|" 
> sapply(res["//Hit_len"], xmlValue)
 [1] "232" "388" "397" "402" "456" "402" "388" "388" "388" "388"
>

ADD COMMENT • link 8.8 years ago Martin Morgan 25k

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Thanks a lot. Is there anyway to give NCBI accession number (eg: ''O48946") as an input instead of the sequence?

ADD REPLY • link 8.8 years ago maahpishanu • 0

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Use the accession number(s) as the query

> res = blastSequences("O48946", "nr", program="blastp", as="XML")
> sapply(res["//Hit_id"], xmlValue)
 [1] "gi|15236786|ref|NP_194967.1|"     "gi|297798722|ref|XP_002867245.1|"
 [3] "gi|565449881|ref|XP_006285557.1|" "gi|727512843|ref|XP_010432725.1|"
 [5] "gi|727549104|ref|XP_010447394.1|" "gi|567217696|ref|XP_006412477.1|"
 [7] "gi|674237085|gb|KFK29850.1|"      "gi|922532521|ref|XP_013597875.1|"
 [9] "gi|674960897|emb|CDX72357.1|"     "gi|674919795|emb|CDY13484.1|"    
> res[["//BlastOutput_query-ID/text()"]]
gi|73917709|sp|O48946.1|CESA1_ARATH 
> res[["//BlastOutput_query-ID/text()"]]
gi|73917709|sp|O48946.1|CESA1_ARATH

ADD REPLY • link 8.8 years ago Martin Morgan 25k

score 0 · Answer 2 · 2016-02-05

I found that I can send my query like the following through R:

system2('blastp',c('-remote', "-best_hit_overhang", "0.1", "-best_hit_score_edge", "0.1",'-db', "'refseq_protein'" ,'-entrez_query', "prf||O48946"),stdout=TRUE)

However, I get the following error:

[1] "Error: (301.23) [CONN_Read(blast4/HTTP; http://www.ncbi.nlm.nih.gov/Service/dispd.cgi?service=blast4&address=W7DELL902035.mpimp-golm.mpg.de&platform=i386-pc-win64)]  Unable to read data: Timeout[30.000000]"
[2] "Warning: Error initializing remote BLAST database data loader: Protein BLAST database ''refseq_protein'' does not exist in the NCBI servers"                                                                  
[3] "Command line argument error: Query is Empty!"                                                                                                                                                                 
attr(,"status")
[1] 1
Warning message:
running command '"blastp" -remote -best_hit_overhang 0.1 -best_hit_score_edge 0.1 -db 'refseq_protein' -entrez_query prf||O48946' had status 1

Could anybody help me with this?