Hi,
I think there is a simple solution to this question, but I can't seem to figure it out.
When doing a batch blast with the online tool (NCBI blastn) I can download the blast report (hit table.csv), which list all the info one would want (match score, E value, cover length etc.) but it only gives the accession numbers for the reference sequence.
This is of little help, because then I have to look up everything manually anyway, to know what it is (I am blasting approx. 100 sequences, so this is not feasible).
I am sure there is a simple solution - Anyone who knows how to get the full annotation to the hits?
Best wishes,
Mathilde
Dear Mathilde, below BLAST button there is "Algorithm parameters" after opening this link, there is "Max target sequences" you can change the search parameters.
Best regards.
I don't think you can solve this on the website. For what I remember, blast simply does not consider the title of the sequences after the first blank space, so there is not annotation in the output. Possible solutions I used over the years are mainly:
1. if possible (it depends on the size of the database) build your own database but replace blanks in the sequence titles used to build the database, magically the annotations will appear in the output (but you'll have to run the blast from the command line that can be annoying without (some) computer science skills.
2. if you use unix based computer, you could try to grep the sequence file used for database construction using the sequence id in your truncated output. I don't know if there is a similar tool in dos on windows, tough.
3.cut the column of identifiers for the subject sequences from the csv and paste it in ncbi protein/nucleotide (depending what you have) and get all the summary records for the sequences. the above output can be used with lookup functions in excel to replace the truncated id with the full ones (see vlookup for instance).
Thank you for your answers - I am always so impressed when people take the time, thanks a lot!
A colleague of mine had a custom script that could do it, you can find it here: https://github.com/Gurdhhu/bioinf_scripts
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