I have a protein motif or site, which I like to identify in an DNA sequence (multiple fasta file). The motif is N-X-S/T (X!=P), which means Asn, followed by any amino acid but not Pro, followed by Ser or Thr. Also X should not be STOP. So I would like to find all the 3 codon combinations for this site in DNA (9 nucleotides).
I was first thinking of getting the motif written in DNA using IUPAC coding, but that seemed not possible. Writing out all possibilities seems like a too hard task, so I thought there might be a tool which can do this? Any suggestions?
1 answer
Haven't tried it, but you could do a 2-tiered grep-approach. Make sure your fasta is not line-wrapped.
grep -o "AA[CT][ACGT]\{3\}\([AU]C[ACGT]|AG[CU]\)" fasta_file | grep -v "[ACGT]\{3\}CC[ACGT][ACGT]\{3\}".
Assuming Asn = AAY = AA[CU], Ser = UCN, AGY = UC[ACGT], AG[CU], Thr = ACN = AC[ACGT], and Pro = CCN = CC[ACGT],
the first part should match all peptides N-X(traditional = all amino acids)-S/T, the second should get rid off the ones that contain proline in the central position. I am not sure about whether you have to use an additional set of \(\) in the first expression.
The backslash escapes special characters, so that they are not expanded by the shell. I never really understand which characters need to to be escaped and which don't... This post gives an overview but some stuff ("may need to be quoted under certain circumstances.") just feels as if one has freshly escaped from an asylum...
No worries about the backslashes @cschu181, every user (OP) is responsible to double check if the code given here as answer really does the trick (or tweak a little). In this case I could use your approach (and I liked it, especially the grep -v part). I actually modified it a bit, but the idea was certainly yours. I ended up using fuzznuc (from EMBOSS) with your pattern suggestion, and then grep -v to get rid of the Proline patterns.
fuzznuc -pattern AA[CT]NNN[AT]CN -sequence fasta.fa -outfile prog_pattern_1.txt
fuzznuc -pattern AA[CT]NNNAG[TC] -sequence fasta.fa -outfile prog_pattern_2.txt
cat prog_pattern_1.txt prog_pattern_2.txt | grep -v "[acgt]\{3\}cc[acgt][acgt]\{3\}" > prog_pattern_no_Pro.txt
So thanks for the help!
Log in to answer this question.
-
Blog: Google launches Bard (and it fails the translation test :)
written by Michael Dondrup
-
Missense Mutation Function
written by eda •
-
From amino acid sequence to DNA sequence using Reverse Translate software
written by Student •
-
Replace Ambigious codons with Amino acid sequences
written by waqaskhokhar999
-
Help translating RNA to amino acid sequence
written by biocoding4444 •
-
Python: Optimizing my amino acid % composition code
written by michaelrw10 •
-
Translation of Codons into amino acid sequence
written by katherinebridges99 •
-
Reading CDS regions from a gbk file and counting amino acid codons in Biopython
written by cameronmartino •
-
Multiple asterisks inside amino acid fasta sequences
written by Louis Kok •
-
Ambiguous Amino Acid In Motif Search
written by jzabilansky •
Doesn't BLAST(P) already support certain redundant characters?
I'm not sure you'll be able to define all of those exactly, since typically
Xmeans any amino acid (I think), without any restriction. You may not be able to find an alphabet that supports all of what you need.You could maybe blast:
NXSandNXT, and then filter the results with a regex to make sure that the next codon is!= *