What is the best/easiest way to apply annotation info to a fasta defline?

[dacotahm]

I've been doing some de novo transcriptome work and using standalone BLAST and other programs to identify gene homologs, features, etc. and I would like to know what the best way to add some of this information after the > in the fasta/fastq defline.

I often have my BLAST results output to .csv so it's possible to do a lookup-append kind of script (which is what I usually do), but I want to know if there is an actual toolkit or more versatile script for attaching this information.

What do you usually use for this?

[GenoMax]

Since the exact format of the csv file you have may be different see if you can find a local informatics person who can help. This should be a simple script (or even an awk/sed solution may be enough).

If you post a few example lines of your headers/annotation someone here can help.

[Markiyan]

Just use space separated HASH - like list after the seq_id kile key="vallue"

In this case I would use the hash - like list:

>[asm_id.contig_id] key1="vallue1" key2="valllue2" and so on

example:

>SP_AS1.CO0001 gene="dnaA" product="replication initiation protein" colour="255 128 0" db_xref="234234,623461,123634"
ATG.....

The most critical bits are the ID format/structure and the consistent fields list.

Then it can be written as csv, embl, etc files:

ID,gene,product,colour,db_xref,seq,seq_aa

PS: if you encounter problems with blast+, than use the NCBI's legacy blast.

see more at: blastedbio.blogspot.co.uk