SMITHWATERMAN(1)

✨ SMITHWATERMAN ✨

okay bestie, welcome to smithwaterman — the local sequence alignment girlie from User Commands 💅 she's here to find similar regions between two strings, or between nucleotide or protein sequences. no cap.

🎀 SYNOPSIS 🎀

smithwaterman [options] <reference sequence> <query sequence>

🦋 DESCRIPTION 🦋

so like. the Smith–Waterman algorithm does local sequence alignment. what does that mean fr fr? it means she's out here determining similar regions between two strings, or between nucleotide or protein sequences. 🌸

and here's the iconic part: instead of looking at the total sequence like some basic algorithm, Smith–Waterman compares segments of all possible lengths and optimizes the similarity measure. she's thorough. she's giving main character energy. she ate. 👑

💖 OPTIONS 💖

• -m, --match-score — the match score (default 10.0) ✨
• -n, --mismatch-score — the mismatch score (default -9.0) 😭
• -g, --gap-open-penalty — the gap open penalty (default 15.0) 🫶
• -z, --entropy-gap-open-penalty — enable entropy scaling of the gap open penalty 🌈
• -e, --gap-extend-penalty — the gap extend penalty (default 6.66) 💀
• -r, --repeat-gap-extend-penalty — use repeat information when generating gap extension penalties 🔥
• -b, --bandwidth — bandwidth to use (default 0, or non-banded algorithm) 🧚
• -p, --print-alignment — print out the alignment 💅
• -R, --reverse-complement — report the reverse-complement alignment if it scores better 🔄

🌟 so what does she actually print 🌟

when you call her with literal reference and query sequences, smithwaterman prints the cigar match positional string and the match position for the query sequence against the reference sequence. that's the whole vibe. 💜

👑 AUTHOR 👑

this manpage was written by Andreas Tille for the Debian distribution, and can be used for any other usage of the program. iconic of him honestly 🎀

mwah 💋 that's a wrap — this was smithwaterman 0.0+20151117, dated June 2016, and yes she's still that girl. bye bestie, go align something 🦋✨