Alignment

Perform sequence alignment to a reference genome or to other sequences in a database

align

Aligns a given sequence to a reference genome using a specified alignment algorithm.

Usage:

import GenBioX.alignment as a

a.align(seq, ref, algorithm='global')

Maps high-throughput sequencing reads to a reference genome to identify their genomic location and alignment quality.

Usage:

a.read_alignment(reads, reference_genome)

performs pairwise_alignment of two sequences

Usage:

a.pairwise_alignment("seq.fasta", "seq2.fasta")

Merges two sequence alignments to produce a single alignment.

Usage:

a.merge_alignments(aln1, aln2)

Evaluates the quality of a sequence alignment based on various metrics such as coverage, accuracy, and gap distribution.

Usage:

aln_quality = a.evaluate_alignment_quality(alignment)
print(aln_quality)

Extracts conserved regions from a multiple sequence alignment.

Usage:

conserved_regions = a.extract_conserved_regions(alignment)
print(conserved_regions)