Biopython - calculate overlap between two sequences

Question

[Am.A]

is there a function or code that takes a sequence and check for overlap by 80% to 90% with a multi-fasta file

Answer 1

[chen]

This overlap analysis is a built-in function of OpenGene in Julia (https://github.com/OpenGene/OpenGene.jl)

julia> using OpenGene, OpenGene.Algorithm

julia> r1=dna("TTTAGGCCTGTCACTGTGAACGCTATCAGCAAGCCTTTGCATGATTTTTCTCTTTCCCACTCCTACATTCTCGGTGATGACAACAACTGTAGCCTGATCCAGATATTTCGAAGTGCAACAAATCGTATTCAATATAGAGTAAGG")
dna:TTTAGGCCTGTCACTGTGAACGCTATCAGCAAGCCTTTGCATGATTTTTCTCTTTCCCACTCCTACATTCTCGGTGATGACAACAACTGTAGCCTGATCCAGATATTTCGAAGTGCAACAAATCGTATTCAATATAGAGTAAGG

julia> r2=dna("GTTAGCTATTACTGTAATCACCGCGAGACAAGTTAATGAGAGAGTTATTCATAAAACTTACTCTATATTGAATACGATTTGTAGCACATCGAAATATCTGGATCAGGCTACAGTTGTAGTCATCACCGAGAATGTAGGAGTGG")
dna:GTTAGCTATTACTGTAATCACCGCGAGACAAGTTAATGAGAGAGTTATTCATAAAACTTACTCTATATTGAATACGATTTGTAGCACATCGAAATATCTGGATCAGGCTACAGTTGTAGTCATCACCGAGAATGTAGGAGTGG

julia> offset, overlap_len, offset = overlap(r1, r2)
(56,88,4)

julia> merged = simple_merge(r1, r2, overlap_len)
dna:TTTAGGCCTGTCACTGTGAACGCTATCAGCAAGCCTTTGCATGATTTTTCTCTTTCCCACTCCTACATTCTCGGTGATGACAACAACTGTAGCCTGATCCAGATATTTCGAAGTGCAACAAATCGTATTCAATATAGAGTAAGGTTTATGAATAACTCTCTCATTAACTTGTCTCGCGGTGATTACAGTAATAGCTAAC

And overlap analysis is also included in AfterQC, which is written in Python (https://github.com/OpenGene/AfterQC)

Maybe this overlap function can be added to BioPython