Hello, is there an easy way to retrieve the sequences from the hits in the blastn output? I just need the sequences without the gap insertions "-". Thank you.
-
-
Look at the "blastdbcmd" program examples on this page. http://www.ncbi.nlm.nih.gov/books/NB...BLAST_search_r .. if you are looking to retrieve the subject sequences.Last edited by GenoMax; 06-19-2013, 08:06 AM. -
Thank you GenoMax. I tried using blastdbcmd but for some reason it doesn't seem to be working as described on that page.
I have downloaded the Gallus 4 genome from NCBI and ran makeblastdb using blast+ 2.2.25. When I run:
blastdbcmd -db gga_ref_Gallus_gallus-4.0_all.db -entry all | grep ">" | head
I get:
>gnl|BL_ORD_ID|0 gi|358485511|ref|NC_006088.3| Gallus gallus breed Red Jungle fowl, inbred line UCD001 chromosome 1, Gallus_gallus-4.0, whole genome shotgun sequence
>gnl|BL_ORD_ID|1 gi|358485510|ref|NC_006089.3| Gallus gallus breed Red Jungle fowl, inbred line UCD001 chromosome 2, Gallus_gallus-4.0, whole genome shotgun sequence
>gnl|BL_ORD_ID|2 gi|358485509|ref|NC_006090.3| Gallus gallus breed Red Jungle fowl, inbred line UCD001 chromosome 3, Gallus_gallus-4.0, whole genome shotgun sequence
>gnl|BL_ORD_ID|3 gi|358485508|ref|NC_006091.3| Gallus gallus breed Red Jungle fowl, inbred line UCD001 chromosome 4, Gallus_gallus-4.0, whole genome shotgun sequence
>gnl|BL_ORD_ID|4 gi|358485507|ref|NC_006092.3| Gallus gallus breed Red Jungle fowl, inbred line UCD001 chromosome 5, Gallus_gallus-4.0, whole genome shotgun sequence
>gnl|BL_ORD_ID|5 gi|358485506|ref|NC_006093.3| Gallus gallus breed Red Jungle fowl, inbred line UCD001 chromosome 6, Gallus_gallus-4.0, whole genome shotgun sequence
>gnl|BL_ORD_ID|6 gi|358485505|ref|NC_006094.3| Gallus gallus breed Red Jungle fowl, inbred line UCD001 chromosome 7, Gallus_gallus-4.0, whole genome shotgun sequence
>gnl|BL_ORD_ID|7 gi|358485504|ref|NC_006095.3| Gallus gallus breed Red Jungle fowl, inbred line UCD001 chromosome 8, Gallus_gallus-4.0, whole genome shotgun sequence
>gnl|BL_ORD_ID|8 gi|358485503|ref|NC_006096.3| Gallus gallus breed Red Jungle fowl, inbred line UCD001 chromosome 9, Gallus_gallus-4.0, whole genome shotgun sequence
>gnl|BL_ORD_ID|9 gi|358485502|ref|NC_006097.3| Gallus gallus breed Red Jungle fowl, inbred line UCD001 chromosome 10, Gallus_gallus-4.0, whole genome shotgun sequence
But when I try running:
blastdbcmd -db gga_ref_Gallus_gallus-4.0_all.db -entry 358485511
I get:
Error: 358485511: OID not found
BLAST query/options error: Entry not found in BLAST database
The entry seems to be there so why can't blastdbcmd recognize it when I try to query it?Comment
-
Did you run makeblastdb with '-parse_deflines' ?savetherhino.orgComment
-
Ok I just ran makeblastdb with the -parse_seqids option and it works now. What is the difference between parse_seqids and parse_deflines?Comment
-
Sorry, -parse_seqids is the flag I was thinking..Originally posted by rkizen View Postsavetherhino.orgComment
-
See http://blastedbio.blogspot.jp/2012/1...cbi-blast.html for my thoughts on the difference between the NCBI style IDs and free-format user provided identifiers (and the problems using them with blastdbcmd).Comment
-
Researchers using sequencing and genomics tools often have to make trade-offs. They can choose between speed or scale, short reads or long-range information, or targeted panels or a view of the whole transcriptome. New technologies that have been released this year are built to address those tough choices.
We asked six companies the same four questions to learn about their latest products. The new technologies bring a lot to the table, including rethinking sequencing... -
The immune system’s power comes from its genetic diversity, allowing myriad threats to be neutralized through first recognizing foreign antigens. That diversity is also what makes the immune system so difficult to study. Recent advances in sequencing technology and computational biology, however, are giving researchers new tools to understand immune responses and immune-related diseases in greater detail.
This convergence of genetics, immunology, and computation...09-01-2026, 05:41 AM
Comment