I have a text file including multiple primer sequences and I want to blast the SSR primers against the genome to see what degree the genetic map can be anchored to the reference genome.
I want to convert the text file into fasta file, can I manually add a ">" in the first line before each primer sequence?
Thanks
You can do it with computer programs like MEGA and also you can use online convert sites. Actually i use http://sing.ei.uvigo.es/ALTER/ for online data file conversation.
In the text file, get rid of any information that is not the taxon name or the sequence, and then format it as:
>taxon_name
sequence
Reem Alhamidi
I think new link is ; http://www.sing-group.org/ALTER/
How did you use BioEdit software to change into Fasta format?
Qiang Wei
Kashif Ahmad
You can open the text. file using Bio Edit then save it as a type of FASTA.
I also need to find a way to convert .txt to .fasta files. I am on Mac so ClustalX and BioEdit are not available. I was able to input my .txt file into Mega and save it as a .fasta file, but it produced a .fasta.meg file with a #Mega header and a .meg file type, which Blast+ does not recognize.
Any other options?
http://www.opiniomics.org/converting-from-genbank-format-to-fasta-using-microsoft-excel/
This may work
Hi,
You certainly have already found plently of info. Nevertheless, I would like to add a couple of good resources in this regard- just in case someone still needs them.
A nice collection of many web links for data conversion:
https://molbiol-tools.ca/Convert.htm
Easy-to-use link for conversion:
https://www.hiv.lanl.gov/content/sequence/FORMAT_CONVERSION/form.html
Regards
The examle from Muhammad Afzal was very easy to use, and requires no downloading of any specific programs because it is all done for free online. I used this link here and directly copied and pasted my reads from a text file to generate a fasta
https://www.hiv.lanl.gov/content/sequence/FORMAT_CONVERSION/form.html
Thanks for all of your excellent suggestions and input. It turns out, it was much easier than I had thought. In my situation, I was trying to mine information from a new predictive whole genome annotation from a non-model non-photosynthetic plant. I was interested to see which functional proteins were present in the plant. So I chose metabolic pathways and enzymes that I hypothesized to still be present and functional in the plant, went through GenBank and Swiss Uniprot and downloaded protein sequences in fasta format that I could blast against my annotation. My problem was that Blast+ did not recognize .doc or .txt files as a fasta file, even though all of the sequences were in fasta format. I solved the problem by using TextEdit. Go to Format-Make Plain Text and save the tile as .txt file. You can then change the name exchanging .txt for .fasta and Blast+ will recognize the file as a fasta file ( e.g. change proteins_of_interest.txt. to proteins_of_interest.fasta). If you need to edit the file again, simply exchange the .fasta for .txt, make your edits, save the file as a .txt. file and then change the .txt back to .fasta.
I am a Mac user as well, Steven Miller . I tried your method and it works like a charm. Thanks for the input Sir.
Actully, you can. The > sign and following text are the indicator of fasta files.
The EASIEST way to convert .txt to .fasta is by
1) Go to the file explorer that you .txt file is located
2) Click 'View'
3) Click 'Show'
4) Click 'File name extensions'
As of right now, you will see the extension of every file in that folder and you can simply change .txt to .fasta by typing
I tried https://www.hiv.lanl.gov/content/sequence/FORMAT_CONVERSION/form.html before my friend told me this method and it messed up my file so bad.
By simply change you file extension, it might add some quotation marks in your file. But you can just 'Replace' the quotation marks with nothing (leave 'Replace with' blank). You must remove the quotation marks otherwise those sequences won't be uploaded onto the program like Proteome Discoverer.
Btw, the FASTA file contains '>' followed by 'Name of your sequence' and your sequence should be in the next line. > tells the program the following line is the sequence which named as the text follows >.
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