Automated Blasts
Alan Sinclair
Saturday, 15 August 2009 00:26 UTC
Hi, does any know of a piece of software that will allow me to perform automated blasts on NCBI? My specific needs is one that can open hyperlinks from word> is then capable of then translating the nucleotide sequence into an amino acid sequence> which can then be pasted into tblastn with the results from the blasted being pasted into a new word document. I realise the scope of what I am asking here but consider this;
Currently I am looking for protein homologues in the EST database of others, so I input my confirmed amino acid seq. and blast on tblastn. Once the blast is completed I select those hits that are significant, paste them into word and then reciprocally blast the translation of each of them against my model organism to ‘confirm’ if the protein is valid. The problem is that I have perhaps 100 proteins to blast, with maybe 100 significant hits returned from each initial blast which then all need to be reciprocally blasted. That’s upwards of 10,000 individual blasts before taking into account additional blasts that will envitably follow through further lines of enquiry! It makes me weak thinking about doing them manually.
I have also started to dable in programming, specifically perl, however I have little to no experience in programming so producing a script capable of performing what I need is unfortunatley quite a long way off. Which is why I have come here. Advice much appeciated.
Alan
Updated 15 August 2009 00:28 UTC
-
Replies
-
Hi Alan,
There are many software in the market related sequence analysis and blasting with many features like “Genchek” by OcimumBiosolution .using that you can save your results in your working folder and directly you can blast it again, no need to save in word.
Best regards,
ATul.
-
For your questions, I think you can use the program from Inparanoid (inparanoid.sbc.su.se/). You need to send an email to them to get a stand-alone version. And you can send your problems to them. I think the Inparanoid program need to be a little bit modification for your problem.
Yu
-
Thank you for the response, all very helpful. Keep them coming!!
-
I should say that most of the species which I am blasting against are not fully sequenced so the EST represent all the genetic information publicably available for that species.
-
Dear Alan Sinclair,
If you need to automate these many requests I would seriously consider doing it locally on your computer and taking the time to learn a bit more of programing. If you like perl then try using bioperl. It has several modules to do all sorts of sequence analysis, including local blast. It will take some effort but in a few weeks you will be able to do what you need to and acquire a set of very useful skills for the future.
If that sounds like too much work, then I would second the suggestion of setting up Inparanoid.
-
