BLAST export library 'annotate'
2
0
Entering edit mode
b.stielow • 0
@bstielow-7046
Last seen 6.9 years ago

Hi all,

i m trying to export the results of a simple BLASTn query (16S ribosomal RNA) against Genbanks nr database using library 'annotate' and the function 'blastsequences' (see: http://www.bioconductor.org/packages/release/bioc/manuals/annotate/man/annotate.pdf)

Function works well, hitlist is retrieved correctly as dataframe or multiple alignment, but there is no way to write the results into Fasta format!(?) I found hints that this might be possible via 'Biostrings' (which is essential part of the function). Can anyone provide a solution for this? Help is much appreciated!

Best regards,

Benjamin

 

See example below:

library(Biostrings)
library(annotate)
blastSequences(x = "AGTTTGATCATGGCTCAGATTGAACGCTGGCGGCAGGCCTAACACATGCAAGTCGAACGGTAACAGGAAG
CAGCTTGCTGCTTTGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGA
TAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGCACAAAGAGGGGGACCTTAGGGCCTCTT
GCCATCGGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACGGCTCACCTAGGCGACGATCCCTAG
CTGGTCTGAGAGGATGACCAGCAACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTG
GGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCCATGCNGCGTGTATGAAGAAGGCCTTCGGGTTGT
AAAGTACTTTCAGCGGGGAGGAAGGGAGTAAAGTTAATACCTTTGCTCATTGACGTTACCCGCAGAAGAA
GCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGC
GTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATCTG
ATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCT
GGAGGAATACCGGTGGCGAAGGCGGCCCCCTGGACGAAGACTGACGCTCAGGTGCGAAAGCGTGGGGAGC
AAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGTCGACTTGGAGGTTGTGCCCTTGAGGCG
TGGCTTCCGGANNTAACGCGTTAAGTCGACCGCCTGGGGAGTACGGCCGCAAGGTTAAAACTCAAATGAA
TTGACGGGGGCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGATGCAACGCGAAGAACCTTACCTGGTC
TTGACATCCACGGAAGTTTTCAGAGATGAGAATGTGCCTTCGGGAACCGTGAGACAGGTGCTGCATGGCT
GTCGTCAGCTCGTGTTGTGAAATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTATCCTTTGTTGCCA
GCGGTCCGGCCGGGAACTCAAAGGAGACTGCCAGTGATAAACTGGAGGAAGGTGGGGATGACGTCAAGTC
ATCATGGCCCTTACGACCAGGGCTACACACGTGCTACAATGGCGCATACAAAGAGAAGCGACCTCGCGAG
AGCAAGCGGACCTCATAAAGTGCGTCGTAGTCCGGATTGGAGTCTGCAACTCGACTCCATGAAGTCGGAA
TCGCTAGTAATCGTGGATCAGAATGCCACGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACA
CCATGGGAGTGGGTTGCAAAAGAAGTAGGTAGCTTAACTTCGGGAGGGCG
" ,database = "nr", hitListSize="20", program = "blastn", as="data.frame")

 

blast annotate biostrings export fasta • 1.0k views
ADD COMMENT
2
Entering edit mode
@branislav-misovic-4248
Last seen 2.4 years ago
Netherlands/Amsterdam

 Hi Benjamin

 when you search for function it is good to list functions in the packages you already use  or type "??fasta "  or  search R.docs website.  Biostrings developers made already writeXStringSet
(In your example i used only first 70 NN as i hoped response from website would be faster ... )

library(annotate);
library(Biostrings) ;ls("package:Biostrings")

BLrez =blastSequences(x = "AGTTTGATCATGGCTCAGATTGAACGCTGGCGGCAGGCCTAACACATGCAAGTCGAACGGTAACAGGAAG" ,database = "nr", hitListSize="20", program = "blastn", as="data.frame")
 
BLfasta = DNAStringSet (BLrez$Hsp_hseq)
names (BLfasta) = as.character(BLrez$Hit_id)
 
writeXStringSet (BLfasta, file="rRNA.fasta.txt", format="fasta", width=80)


btw. great  R & sequencing tutorial (bit old)  is here .
Branko

 

ADD COMMENT
0
Entering edit mode
b.stielow • 0
@bstielow-7046
Last seen 6.9 years ago

Dear Branko,

thanks so much for your help, very much appreciated, that worked perfectly! Actually i already came across 'writeXStringSet' but struggled with its use. Thanks again!

Best regards,

Benjamin

ADD COMMENT

Login before adding your answer.

Traffic: 251 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6