Tweet
I'm a Mol Biol resercher and I'm new handling sequences. I need to find sequences of specific genes in a multifasta file from Roche 454. How can I do it?. Is there software for this under Windows? Thaks
-
-
Simplest way would be to use the "blast 2 sequences" tool from NCBI Blast search page. Go to http://blast.ncbi.nlm.nih.gov/ and then scroll down to "Specialized BLAST" section.
Select Align two (or more) sequences using BLAST (bl2seq). Both sequence files will need to be in the multi-fasta format though. You could also provide accession numbers, GI # for the genes you are looking for instead of the actual sequence. -
Thanks, now I'm doing that, but it is very slow and we prefer perform alignments in a local machine. Is this possible in a Win platform?Comment
-
Hello,
If you can handle a bit the command line, I think the minimal number of steps to run blast locally are:
1- Download blast executables for your system from
ftp://ftp.ncbi.nlm.nih.gov/blast/exe...blast+/LATEST/
2- Move to the directory where you have the executables. Prepare database of your 454 sequences (e.g. multifasta454.fa). On windows it could be something like
3- Blast your query file (genes) against the database aboveCode:cd "C:/Program Files/blast+/ncbi-blast-2.2.26+/bin/" makeblastdb -in path/to/multifasta454.fa -dbtype nucl
Blastn has a lot of options for fine tuning how you want to find matches and how to report results.Code:blastn -query path/to/query.fa -db path/to/multifasta454.fa -out path/to/myoutput.blastout
Hope this helps
DarioComment
-
Thank you Dario, I'll try.Comment
-
Data variability is still an issue in sequencing technologies despite the advances in reproducibility and accuracy of these platforms. But the problem does not originate in the sequencing itself, but in the previous steps, before the sample reaches the sequencer.
The first step is collection, followed by preservation and sample preparation for analysis. Most scientists overlook those steps, but not being careful might just be skewing the experiment’s results.
...06-02-2026, 10:05 AM -
With the launch of new single-cell sequencing platforms in 2026, the field stands at an exciting inflection point. This article surveys the most impactful advances in the field and discusses how they’re reshaping research in cancer, immunology, and beyond.
Introduction
Single-cell sequencing technologies have undergone remarkable advances over the past decade, transitioning from low-throughput experimental approaches to highly scalable platforms capable of...05-22-2026, 06:42 AM
Comment