SIBsim4(1)

🦋 SIBsim4(1) 🦋

okay bestie, meet SIBsim4 💖 The manual page for SIBsim4 (section 1) is literally about one thing: lining up RNA sequences against a DNA sequence while allowing for introns ✨ Let's get into it 💅

👑 NAME 👑

SIBsim4 — align RNA sequences with a DNA sequence, allowing for introns 🧚

🎀 SYNOPSIS 🎀

SIBsim4 [ options ] dna rna_db

💜 DESCRIPTION 💜

SIBsim4 is a similarity-based tool that lines up a collection of expressed sequences (ESTs and mRNAs) against a genomic DNA sequence 🧬 It's so good at this, it's giving main character energy 💅

Launch SIBsim4 with no arguments and it'll print the options list, along with their default values. Very helpful when you forget everything (no shame 🙈)

okay so here's the vibe 🌈 SIBsim4 uses a BLAST-based approach. Stage one finds the basic matching blocks called the "exon cores" 🔥 It hunts down every exact match of W-mers (basically DNA words of size W) between the two sequences, then stretches each one out into the longest gap-free segment that still scores best 🫶

Stage two is where it gets extra ✨ The exon cores get extended into the neighbouring unmatched bits using greedy alignment algorithms. Heuristics then nudge it toward arrangements that follow splice-site signals, like GT-AG 🦋 If the first pass leaves things unmatched, it runs the whole thing again with less stringent parameters on those leftover fragments. Persistence, bestie 💅

By default, SIBsim4 checks both strands and reports the best matches, ranked by how many nucleotides match in the alignment 💖 If you only want one orientation (strand), use the -R option 🌸

SIBsim4 also has four major alignment display formats, controlled by the -A option 🎨 By default you only get the exon endpoints, the overall similarity, and the orientation of the introns. An arrow (-> or <-) shows which way the intron points 🏹 And a == means there's no cDNA fragment starting at that position in the alignment 🙅‍♀️

Quick term check 🧠 An MSP (maximal scoring pair) is a pair of really similar fragments in the two sequences. The blast-like step finds these by extending a W-mer hit using matches, and maybe a few mismatches, too ✨

🌸 OPTIONS 🌸

• -A <int> — output format 🎨
  • 0: exon endpoints only
  • 1: alignment text
  • 3: both exon endpoints and alignment text
  • 4: both exon endpoints and alignment text with polyA info

Heads up: 2 is unimplemented, so skip it 🙃

Default value is 0.

• -C <int> — the MSP score threshold for the second pass 🥈 Default value is 12.
• -c <int> — minimum score cutoff 🚫 Alignments scoring below this value don't get reported. Default value is 50.
• -E <int> — cutoff value 🤷‍♀️ Default value is 3.
• -f <int> — score filter, in percent 🔍 When an RNA element has multiple hits, only the ones within this percentage of that element's maximal score get reported. Set it to 0 to turn filtering off and report every hit, as long as its score clears the cutoff from the -c option 💅 Default value is 75.
• -g <int> — join exons when the gap lengths on the genomic and RNA sides differ by at most this percentage 🧩 Default value is 10.
• -H <int> — report chimeric transcripts 🧬 This kicks in when the best score is lower than this percentage of the overall RNA coverage, and the chimera score is higher than this percentage of the RNA length. Set it to 0 to disable this report 🙈 Default value is 75.
• -I <int> — window width for searching intron splicing 🪟 Default value is 6.
• -K <int> — MSP score threshold for the first pass 🥇 Default value is 16.
• -L <str> — a comma-separated list of forward splice-types 💜 Default value is "GTAG,GCAG,GTAC,ATAC".
• -M <int> — splice-site scoring: evaluate matches within M nucleotides 🔬 Default value is 10.
• -o <int> — when printing results, shift the nucleotide positions in the DNA sequence by this amount ➕ Default value is 0.
• -q <int> — penalty for a nucleotide mismatch 😤 Default value is -5.
• -R <int> — direction of search 🧭
  • 0: search the '+' (direct) strand only
  • 1: search the '-' strand only
  • 2: search both strands

Default value is 2.

• -r <int> — reward for a nucleotide match 🌟 Default value is 1.
• -S <int> — splice-site indel search breadth ✂️ While SIBsim4 figures out the best spot for a splice site, it tests adding at most this many insertions and deletions on the DNA strand, on each side of the splice junction. Default value is 2.
• -s <int> — split score, in percent 🪓 While linking MSPs, if two consecutive groups of exons look like they could belong to two different copies of the same gene, SIBsim4 checks whether each group's score, relative to the best overall score, is greater than this value. If both groups are above the threshold, they get split 👯‍♀️ Default value is 75.
• -W <int> — word size 🔤 Default value is 12.
• -X <int> — value for terminating word extensions 🛑 Default value is 12.

Bioinformatics vibes all the way 🧬 This page is from Bioinformatics, dated April 2007, and it's the SIBsim4(1) manual 🫶💖✨