Dear all,
I have a file including thousands of sequences for a special plant species.
I want to obtain their corresponding gene IDs. I know that the best way of doing this is to perform blast, but since the number of sequences is huge, I am looking for a way to do this automatically.
Do you think all against all blast is a good way? if so can you please give me a clue to do it?
Thank you in advance
Nazanin
•
written
by
nazaninhoseinkhan
1 answer
Assuming you are working with nucleotides, have a local blast installation and your gene reference sequences formatted as a blast database, This could be start of a solution to creating links between your sequences to and known gene IDs.
blastn -db reference.bdb -query file_with all sequences.nt -out result.alignment
But then you will still need to tune your "expect", pick an output format, and eventually interpret the resulting alignments which unless you have a fairly arbitrary policy, is going to be the real work.
Log in to answer this question.
-
Revive old microarray data linking it to new gene annotations
written by lessismore
-
Methylation-Gene expression correlation
written by nazaninhoseinkhan
-
conversion of case_ids to file_ids TCGA data
written by nazaninhoseinkhan
-
how to generate CNVplot from variant effect predictor result
written by nazaninhoseinkhan
-
Annotation of huge number of CNV files
written by nazaninhoseinkhan
-
removing outliers before running DESeq2
written by nazaninhoseinkhan
-
how to characterize microbes in a fastq file of sewage microbiome
written by nazaninhoseinkhan
-
GC percent detection for several number of genes
written by nazaninhoseinkhan
-
How to find targets for large number of lncRNAs
written by nazaninhoseinkhan
-
corresponding gene names for probeIDs
written by nazaninhoseinkhan
Hi,
I see you can run quite easily blast for several sequences at one; http://www.ncbi.nlm.nih.gov/guide/howto/submit-mult-seq-blast/ I'm not sure how scalable this is
You can also limit your search to specific organisms to find just matches for plants.