Hi all,
I am trying to create blast database for protein sequences formatted like this:
>lcl|Bm_nscaf1071_03
MLPIWTSEFLQAVSRMDPKFIALHLQEVGGKAYEKSMQYVKDFVQRLCDC
PELRLFDKIRIYLDEDFSSPEKFTALGNMYFAHSSLVDLKIWDFDLKAYV
DVVGKEIHSGNIENASTKEKAKFPQHFFPEVMSSLYLHLNVLR
>lcl|Bm_nscaf1071_04
MATRLDASWNRWMLTNSTAVPRMVQRVRRNPFRDHLHCNNTAPLGQRSLW
PVTLLAETWDPSFSQGLYPIQLYPYLTPLKTLSSITLTQSHGFKDSIQSN
SNPVSPL
>lcl|Bm_nscaf1071_05
MLQKVTEDLSAQRVQGGAEGGRLQYRRRADQRLVLTVGKKEFAHVDHQKI
FREPWVRDLPTPPSHYRLVSYQGQSGRLVVEGFLARRKRKPSYTASSRRL
QRYDRELEALRPHLFEFPVKFPPTYPFEEDVLLPTHYMKTRCPSWCDRVL
VSQAARPLLHDPPRHDTPRHDTPRHDRRSVTESTDSSSGRASSDSSPARS
when I run this command
makeblastdb -in bmori.fasta -dbtype prot -parse_seqids -out bmori
I am getting this error:
Error: NCBI C++ Exception:
"/home/coremake/release_build/build/PrepareRelease_Linux64-Centos_JSID_01_491_130.14.22.10_9052_1363121432/c++/src/objtools/blast/seqdb_writer/build_db.cpp", line 303: Error: ncbi::s_FixBioseqDeltas() - Protein delta sequences are not supported.
I was able to run this on all other genomes without any problem. Can anybody explain why this is happening?
Thanks very much!
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written
by
arnstrm
3 answers
no problem withmakeblastdb 2.2.28+
$ cat in.fa
>lcl|Bm_nscaf1071_03
MLPIWTSEFLQAVSRMDPKFIALHLQEVGGKAYEKSMQYVKDFVQRLCDC
PELRLFDKIRIYLDEDFSSPEKFTALGNMYFAHSSLVDLKIWDFDLKAYV
DVVGKEIHSGNIENASTKEKAKFPQHFFPEVMSSLYLHLNVLR
>lcl|Bm_nscaf1071_04
MATRLDASWNRWMLTNSTAVPRMVQRVRRNPFRDHLHCNNTAPLGQRSLW
PVTLLAETWDPSFSQGLYPIQLYPYLTPLKTLSSITLTQSHGFKDSIQSN SNPVSPL
>lcl|Bm_nscaf1071_05
MLQKVTEDLSAQRVQGGAEGGRLQYRRRADQRLVLTVGKKEFAHVDHQKI
FREPWVRDLPTPPSHYRLVSYQGQSGRLVVEGFLARRKRKPSYTASSRRL
QRYDRELEALRPHLFEFPVKFPPTYPFEEDVLLPTHYMKTRCPSWCDRVL
VSQAARPLLHDPPRHDTPRHDTPRHDRRSVTESTDSSSGRASSDSSPARS
$ makeblastdb -in in.fa -dbtype prot -parse_seqids -out bmori
Building a new DB, current time: 06/28/2013 18:42:58
New DB name: bmori
New DB title: jeter.fa
Sequence type: Protein
Keep Linkouts: T
Keep MBits: T
Maximum file size: 1000000000B
Adding sequences from FASTA; added 3 sequences in 0.00245404 seconds.
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•
written
by
Pierre Lindenbaum
search for a strange AA using
grep -v ">" *.fasta | sed "s/\(.\)/\1\n/g" | sort | uniq -c
Can you please tell me how exactly you removed the "-" in the protein sequences? When you removed the "-" from the sequences, how can you be sure you are not changing the actual sequence and there by altering the output you will be getting after running blast?
Look for sequences that start with a hyphen - character:
grep '^-'
Remove the leading hyphen:
sed 's/^-//'
These sequences starting with a - character seem to signify a start codon that is created by RNA editing. Can anyone verify?
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written
by
Shaun Jackman
I just encountered this same issue, and at least in my case, these sequences don't represent instances of RNA editing – instead, they're translated pseudogenes: stretches of nucleic acid whose putative translations are found by gene annotation methods that identify homology to known protein sequences, but for which the regions corresponding to the would-be ORF lack the appropriate start and / or stop codons, or have accumulated premature stop codons or frame-shift mutations in the coding sequence.
In my case, especially with sequences containing premature stop codons (indicated by *), simply removing - and * produces nonsensical sequences. I've decided to remove any pseudogene translations.
I have just come across the same issue, and thanks to this post I looked into unexpected characters.
I think my problems originate in this sequence:
>gi|651852200|ref|YP_008869149.1| DNA-binding protein [Streptococcus pneumoniae R6]
-**VWFFFSSVAHSFERIVDGSWMTAKFRSYFSQISVWIISKIVFKSISINFSWFCSFYLVV*LSCFLF*L*PAINGIT*
DLENV*CFCYTTCSLTIRENFFTKIY*ICHKKIIPH
Which makes me suspect it is best to eclude these entries. Possibly not those with a starting - only, in case the Shaun's suggestion regarding RNA editiing is correct, but in case of examples like my own cosmetic corrections will do more harm than good.
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written
by
jcsoellner •
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