Practical report for NORBIS901

Program for pairwise nucleotide sequence alignment using pre-defined anchor

Description

This program aligns pairwise nucleotide sequences with affine penalty model. It divides the two sequences into substring pairs based on the pre-defined "anchor". Anchor sequences may be generated by pattern searching or from prior knowledge. This program applies different combination of gap penalty, Needleman–Wunsch algorithm (global alignment)/ Smith-Waterman algorithm (local alignment) to different substring pairs.

Scheme:

• Anchor sequence : global alignment , anchor penalty score
• Sequence between two anchors: global alignment , general penalty score
• Hanging seqeunce (sequence before the first anchor and sequence after the last anchor): local alignment, general penalty score

PS: Requirement: Python >= 3.7.1

Example usage

python3 alignment_with_anchor.py -f ./example/test2.fa -a ./example/anchor.tsv -ap -1 -am 1 -ago -3 -age -2

Options

usage: alignment_with_anchor.py [-h] -f FA -a ANCHOR [-am A_MATCH]
                                [-ap A_MISMATCH] [-ago A_GAPOPEN]
                                [-age A_GAPEXTEND] [-m MATCH] [-p MISMATCH]
                                [-go GAPOPEN] [-ge GAPEXTEND]

optional arguments:
  -h, --help            show this help message and exit
  -f FA, --fasta FA     fasta file contains 2 sequences
  -a ANCHOR, --anchor ANCHOR
                        anchor file (BED format)
  -am A_MATCH, --anchor_match A_MATCH
                        default = 2
  -ap A_MISMATCH, --anchor_mismatch A_MISMATCH
                        default = -3
  -ago A_GAPOPEN, --anchor_gapopen A_GAPOPEN
                        default = -4
  -age A_GAPEXTEND, --anchor_gapextend A_GAPEXTEND
                        default = -3
  -m MATCH, --match MATCH
                        default = 2
  -p MISMATCH, --mismatch MISMATCH
                        default = -3
  -go GAPOPEN, --gapopen GAPOPEN
                        default = -3
  -ge GAPEXTEND, --gapextend GAPEXTEND
                        default = -1