I am using NCBI to search for protein sequence of certain enzyme. The results were over 1000. How can I get all their fasta format in few quick steps?
Dear Nouran,
What you have to do is when you search for a particular protein, then on the top you can see is "summary 20 per page", change it to 100. Then select all the 100 hits and change display settings on the top to "Fasta(in text)" and click apply. Then you would be able to see all the fasta sequences on the screen which you can just simply save in text file.
Best Regards,
Hi,
under the BLAST header on the page with the results, you have several "buttons", one of which is Download. You can download the entire alignment in one step in several formats. Take a little time and explore the BLAST page and the NCBI for that matter and you will find a lot of useful features.
Enjoy.
Sorry, Siva Kumar and others for trying to maje a point here. In fact, the method of Matej Lexa is the most effective. The first method is something that you have to do more than 10 times in order to get your sequences. Mine and especially Matej Lexa's are few-steps-no-clicking-around-brainlessly methods. As i said sorry for being direct, but anything that goes around clicking is much more appreciated and efficient in this line of work.
Dear Ruxandra,
You have mentioned the way to download the alignment files from Blast but as I understood Nouran doesn't want the alignment nor he is performing the blast. He wants the fasta sequences of all of the hits after searching in ncbi for a particular query. Matej's method may be correct but for a beginner, if you are suggesting a way, then it should be in detail. I don't know whether these cgi scripts are easy or difficult to use. Please don't feel offended.
Best Regards,
Nouran,
As I mentioned that you need to select. There is no need to select the hits. You can also get the desired sequences just by changing the display settings.
Best Regards,
Sorry guys, for the short answer. I was using my phone and could not really type anything complicated or check for other documents. They have many examples on NCBI pages on how to use their scripts. See for example: http://www.ncbi.nlm.nih.gov/books/NBK25500/
For a keyword query this means opening a browsewr and typing something like:
http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=protein&term=anhydrase
This will give you a list of UIDs in an XML format. Just copy the UIDs and put them in a single line of text to get something like:
http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=protein&id=550543572,550543456,550543158&rettype=fasta&retmode=text
This will return a FASTA file
Copying the UIDs manually really spoils this. However, it is easy to write a script that can create the URL for us. If you find a computer with Linux, it will probably have wget, bash and perl already installed. If you call it "try.sh" then by running "./try.sh anhydrase" it will download the FASTA files for you and create a file "anhydrase.fa", plus print the sequences to the terminal.
#!/bin/bash
wget -O uid.xml "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=protein&term=$1"
cat uid.xml | grep "^.Id" | perl -p -i -e "s/.+Id.([0-9]+).+\n/\$1\,/" | perl -p -i -e "chop()" > uid.tmp
ids=$(
Hi, I just want to add that by searching for homologies it is important to realize the percentage of coverage and e-value should be taken in to account. You can gather as much sequences as possible but it might have negative effects when aligning. Moreover, not all database searches give the same results, e.g. when using nr database you get more result whereas using a curated db such as uniprot gives less.
Nonethess, using the latter might give a slightly better alignment result plus these sequences have been checked and described in literature.
Good luck and if you need any more help please dont hesitate and contact me through my email [email protected]
Regards,
René
In the top right there is send to options for getting all in a fasta file. not just 1st page or few pages, but all pages in your search.
Attached is a screenshot
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