Hi, I have a fasta file with hundred of sequences with a 300nt length. I would like to do check what's the similarity of one sequence against all the other sequences. Any suggestion on how to approach this? Thanks
•
written
by
lorenzinip •
2 answers
If your sequences are already aligned and/or the same length, or you do not want to align them, you can use some simple edit distance measures like the Levenshtein distance or other kmer based method.
This will be quick but will be less accurate, and won't necessarily capture meaningful biological patterns, but depending on your use case it may be appropriate.
I keep a few examples of string comparison metrics along with some implementation code here:
https://github.com/jrjhealey/bioinfo-tools/blob/master/StringComparisons.py
Log in to answer this question.
-
Global alignment of protein sequences all x all to identify similarities between them
written by Bruna Avelino •
-
In silico PCR - multiple Primers and multiple sequences at the same time
written by sulichkarolina •
-
De novo motif in DNA sequences
written by Martina •
-
Finding the similarity between two arrays of sequences
written by ririri •
-
Find sequences in a fast files present in another fasta file
written by lorenzinip •
-
Search for sequence homology against various species
written by lorenzinip •
-
Split Large Genome
written by lorenzinip •
-
Calculating the sequence similarity and percentage of matched sequences
written by ago1mutant •
-
How can I align a protein sequence against multiple sequences?
written by bemani_p •
-
Align the oligos with the fasta sequences
written by pabbathi.ranjit •
are you starting from a multiple sequence alignment?
You might have a look at creating distance matrices (eg for phylogenetic studies) , though the 'distance' will often not be in %similarity but will give you a measure of the similarity