I have 42 FASTA files, each containing ~400 amino acid sequences. I want to sort out those sequences which are identical in all 42 files, e.g. sequence of Protein A is identical in all 42 files.. I want to apply Clustal Omega, but there we can input only one file. So if I merge those 42 files, I will not be able to sort out identical sequences one from each file. Kindly guide me in this matter.
Sufian
Hi,
R is probably the way to go, but if you don't want to script things, you can try the ElimDupes tool from HIV database http://www.hiv.lanl.gov/cgi-bin/ELIMDUPES/elimdupes.cgi. I think it can handle large jobs. You can always split the job into a few pieces since you are looking for somethings that are common in all files.
When you use Clustal omega or W, You can copy and paste each FASTA sequence starting with an annotation line (>....) to input multiple sequences for comparison. I think physically copying the FASTA sequences into the input window is easier than uploading files containing FASTA sequences. Good luck.
You want to remove repeated sequences and align the remaining. Is that what you want?
I have standalone Clustal Omega installed on my Linux system. I have around ~400 amino acid sequences of 42 different strains of a single specie (total ~17,000 FASTA sequences). I want know out of those ~400 proteins, which one are common in all 42 strains. For instance, Protein A is identical in all 42 strains, while Protein B is identical in just 35, so I want to exclude Protein B from my data.
Thank you Bin Ma, but I wonder there might be some bioinformatics tool for this job, as there are many tools available for multiple sequence alignment but all are web based, and had a limitation for several hundreds of entries. I found Clustal Omega (standalone version) which could solve this issue, since we can input thousands of sequences, and it can align them within hours.
You could have a look at db toolkit (https://code.google.com/p/dbtoolkit/). It has functionality to merge identical sequences. It could also be used in command line, so writing a script to solve your problem is straightforward !
Let me know if you need help...
its very simpe. You just put all the 42 seuqences in a single text file and upload a ile to ClustalW2.
Then you do not want to align the sequences just to identify those that are found and identical in each of your files. Is that right ?
Pedro Reche: Yes
Rajesh K P: Altogether I have ~17,000 sequences (~400 proteins x 42 strains). Performing MSA of these 17,000 sequences through ClustalW2 will create a huge result. I wont be able to sort out my required data from it.
Kenneth Verheggen: DBToolKit seems nice.
Hi,
R is probably the way to go, but if you don't want to script things, you can try the ElimDupes tool from HIV database http://www.hiv.lanl.gov/cgi-bin/ELIMDUPES/elimdupes.cgi. I think it can handle large jobs. You can always split the job into a few pieces since you are looking for somethings that are common in all files.
Dear Bin Ma,
I have installed R and the package Biostrings.
But, being a newbie, I am having difficulty in learning from the start.
Can you help me in providing a tutorial for performing Multiple Sequence Alignment using Biostrings ?
My objective is to sort out those proteins which are 80% similar in all 42 files (each file containing ~400 amino acid sequences in FASTA format).
Dear all,
I am using following command to perform MSA of 10 protein sequences to get scoring in percentage using Clustal Omega;
clustalo -i seq.faa -o seq-out.faa --percent-d
But I am getting result in the form of Alignment only.
Does anybody know how to get alignment in percentage in Clustal Omega ?
You can use the server at http://imed.med.ucm.es/Tools/sias.html to get identity scores from MSAs
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