SIM4DB(1)

💖 SIM4DB(1) 💖

okay bestie, so this is the manual page for sim4db, living in the General Commands Manual section of your friendly neighbourhood man pages. she's a whole vibe, she aligns cDNA to genomes in batches, and honestly? iconic. let's get into it 🫶

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✨ NAME ✨

sim4db — batch spliced alignment of cDNA sequences to a target genome

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🌸 SYNOPSIS 🌸

a lil baby command line invocation, super simple:

sim4db -genomic g.fasta -cdna c.fasta -scr script -output o.sim4db

where, bestie, let me break it down for you:

• c.fasta and g.fasta are the multi-fasta cDNA and genome sequence files
• script is a script file indicating individual alignments to be computed
• output in sim4db format will be sent to the file o.sim4db (- for standard output)

and if you wanna get fancy with it, a more complex invocation:

sim4db -genomic g.fasta -cdna c.fasta -output o.sim4db [options]

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💅 DESCRIPTION 💅

sim4db performs fast batch alignment of large cDNA (EST, mRNA) sequence sets to a set of eukaryotic genomic regions. no cap. it uses the sim4 and sim4cc algorithms to determine the alignments, but incorporates a fast sequence indexing and retrieval mechanism, implemented in the sister package leaff(1), to speedily process large volumes of sequences. sister package ate, fr fr.

so while sim4db produces alignments in the same way as sim4 or sim4cc, she has additional features to make it more amenable for use with whole-genome annotation pipelines. a script file can be used to group pairings between cDNAs and their corresponding genomic regions, to be aligned as one run and using the same set of parameters. sim4db also optionally reports more than one alignment for the same cDNA within a genomic region, as long as they meet user-defined criteria such as minimum length, percentage sequence identity or coverage. this feature is instrumental in finding all alignments of a gene family at one locus — like, she's a detective 💀. lastly, the output is presented either as custom sim4db alignments or as GFF3 gene features.

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👑 OPTIONS 👑

🌟 Salient options 🌟

• -cdna — use these cDNA sequences (multi-fasta file)
• -genomic — use these genomic sequences (multi-fasta file)
• -script — use this script file
• -pairwise — sequentially align pairs of sequences

if none of the -script and -pairwise options is specified, sim4db performs all-against-all alignments between pairs of cDNA and genomic sequences. yes, everything meets everything. it's giving mixer 😭

• -output — write output to this file
• -gff3 — report output in GFF3 format
• -interspecies — use sim4cc for inter-species alignments (default sim4)

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🎀 Filter options 🎀

• -mincoverage — iteratively find all exon models with the specified minimum PERCENT COVERAGE
• -minidentity — iteratively find all exon models with the specified minimum PERCENT EXON IDENTITY
• -minlength — iteratively find all exon models with the specified minimum ABSOLUTE COVERAGE (number of bp matched) (default 0)
• -alwaysreport — always report <number> exon models, even if they are below the quality thresholds

if no mincoverage or minidentity or minlength is given, only the best exon model is returned. this is the DEFAULT operation.

bestie, listen. you will probably want to specify ALL THREE of mincoverage, minidentity and minlength! don't assume the default values are what you want! 🚨

you will DEFINITELY want to specify at least one of mincoverage, minidentity and minlength with alwaysreport! if you don't, mincoverage will be set to 90 and minidentity to 95 — to reduce the number of spurious matches when a good match is found.

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🦋 Auxiliary options 🦋

• -nodeflines — don't include the defline in the sim4db output
• -alignments — print alignments
• -polytails — DON'T mask poly-A and poly-T tails
• -cut — trim marginal exons if A/T % > x (poly-AT tails)
• -noncanonical — don't force canonical splice sites
• -splicemodel — use the following splice model: 0 - original sim4; 1 - GeneSplicer; 2 - Glimmer; options 1 and 2 are only available with -interspecies. default for sim4 is 0, and for sim4cc is 1.
• -forcestrand — force the strand prediction to always be one of 'forward' or 'reverse'

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🔥 Execution options 🔥

• -threads — use n threads.
• -touch — create this file when the program finishes execution

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💀 Debugging options 💀

• -v — print status to stderr while running
• -V — print script lines (stderr) as they are being processed

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🧚 Developer options 🧚

• -Z — set the spaced seed pattern
• -H — set the relink weight factor (H=1000 recommended for mRNAs)
• -K — set the first MSP threshold
• -C — set the second MSP threshold
• -Ma — set the limit of the number of MSPs allowed
• -Mp — same, as percentage of bases in cDNA

NOTE: if used, both -Ma and -Mp must be specified!

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🌈 SEE ALSO 🌈

• README.sim4db
• http://kmer.sourceforge.net/wiki/index.php/Getting_Started_with_Sim4db
• the sim4dbutils(1) package contains a range of utilities to work with sim4db-generated alignment files, of particular note being convertPolishes(1), filterPolishes(1), mergePolishes(1), and sortPolishes(1)

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and that's the whole page, bestie!! this one's dated January 2016 and she's filed under SIM4DB(1) in the General Commands Manual — go forth and align, you absolute main character 🎀✨💖