Sequence Comparison Using Python/Biopython

Question

[Barby]

Hi all,

Iam quite new in programming!

I need to make a script in order to compare two fasta sequences. I want to find pattern variation in regard to the nucleotides (codons), their position, and of course the related aa.

Any help in this, please?

thanks

[Fabian Bull]

Some further information would be great. Are the sequences in the two files ordered in the same way? Do you want pairwise comparison of all sequences in the 2 files (each against each)? Do you have to use Biopyhton or are other languages possible? Have you ever heard somethin about global alignment?

Answer 1

[Eric Fournier]

You should not be writing any script to compare two fasta sequences. There are tons of alignment software out there, a list of which can be found here. Look under the "pairwise comparison" category.

There are also online tools that you can use, such as bl2seq or CLUSTALW.

Answer 2

[Steve Lianoglou]

Not sure what you really want to do, but here's an example of aligning Amino Acid sequences (in R) taken from Bioconductor's Biostrings library:

R> library(Biostrings)
R> pattern <- AAStringSet(c("HLDNLKGTF", "HVDDMPNAL"))
R> subject <- AAString("SMDDTEKMSMKL")
R> aln <- pairwiseAlignment(pattern, subject, substitutionMatrix="BLOSUM50",
                            gapOpening=-3, gapExtension=-1)
R> aln[1]
  Global PairwiseAlignedFixedSubject (1 of 1)
  pattern: [1] HLDN-----LKGTF 
  subject: [1] SMDDTEKMSMK--L 
  score: 9

R> aln[2]
  Global PairwiseAlignedFixedSubject (1 of 1)
  pattern: [1] HVDD---MPNAL 
  subject: [1] SMDDTEKMSMKL 
  score: 18

R> as.character(aln)
  [1] "HLDN-----LKF" "HVDD---MPNAL"

Biostrings also provides facilities for reading in/out FASTA files. For more information, see:

R> ?pairwiseAlignment