TIGR-BUILD-ICM(1)

💖 TIGR-GLIMMER — General Commands Manual, section (1) 💖

okay bestie, sit down, hydrate, because we're about to talk about tigr-glimmer and it's genuinely so cool. this is the page for the General Commands Manual, section 1, and yes it's giving "bioinformatics but make it cute" ✨

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🌸 NAME 🌸

tigr-glimmer — Creates and outputs an interpolated Markov model(IMM)

no cap, that's the whole vibe. it creates and outputs an interpolated Markov model, aka an IMM. 🧬✨

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🎀 SYNOPSIS 🎀

tigr-build-icm

that's it. that's the whole invocation. so simple, so iconic. 💅

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🦋 DESCRIPTION 🦋

okay so the program build-icm.c creates and outputs an interpolated Markov model (IMM) as described in the paper A.L. Delcher, D. Harmon, S. Kasif, O. White, and S.L. Salzberg. Improved Microbial Gene Identification with Glimmer. Nucleic Acids Research, 1999, in press. 💖

bestie, real talk: please reference this paper if you use the system as part of any published research. it's the polite thing to do and also it's literally the law of academia. 🫶

Input comes from the file named on the command-line. the format? one string per line. each line has an ID string followed by white space followed by the sequence itself. the script run-glimmer3 generates an input file in the correct format using the extract program. slay. 🌈

✨ how the IMM is constructed (the fun part) ✨

so for a given context, say acgtta, we want to estimate the probability distribution of the next character. we shall do this as a linear combination of the observed probability distributions for this context and all of its suffixes, i.e., cgtta, gtta, tta, ta, a and empty. 🌸

and by "observed distributions" I mean the counts of the number of occurrences of these strings in the training set. the linear combination is determined by a set of probabilities, lambda, one for each context string. 👑

for context acgtta the linear combination coefficients are:

lambda (acgtta) (1 - lambda (acgtta)) x lambda (cgtta) (1 - lambda
(acgtta)) x (1 - lambda (cgtta)) x lambda (gtta) (1 - lambda (acgtta)) x
(1 - lambda (cgtta)) x (1 - lambda (gtta)) x lambda (tta) (1 - lambda
(acgtta)) x (1 - lambda (cgtta)) x (1 - lambda (gtta)) x (1 - lambda
(tta))  x (1 - lambda (ta))  x (1 - lambda (a))

we compute the lambda values for each context as follows:

• If the number of observations in the training set is >= the constant SAMPLE_SIZE_BOUND, the lambda for that context is 1.0. ✨
• Otherwise, do a chi-square test on the observations for this context compared to the distribution predicted for the one-character shorter suffix context.
  • If the chi-square significance < 0.5, set the lambda for this context to 0.0.
  • Otherwise set the lambda for this context to: (chi-square significance) x (# observations) / SAMPLE_WEIGHT 💅

not me re-reading that formula three times. it's fine. it's giving math. it ate. 😭

💜 to run the program 💜

build-icm <train.seq > train.model

This will use the training data in train.seq to produce the file train.model, containing your IMM. main character energy fr fr. 🦋

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🌈 SEE ALSO 🌈

bestie, the whole friend group is here:

• tigr-glimmer3 (1)
• tigr-long-orfs (1)
• tigr-adjust (1)
• tigr-anomaly (1)
• tigr-extract (1)
• tigr-check (1)
• tigr-codon-usage (1)
• tigr-compare-lists (1)
• tigr-extract (1)
• tigr-generate (1)
• tigr-get-len (1)
• tigr-get-putative (1),

(yes, tigr-extract shows up twice. we love a repeat appearance. icon behavior. 🙈)

http://www.tigr.org/software/glimmer/

also!! Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer3. it's literally right there, go read it. 📖💖

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🫶 AUTHOR 🫶

This manual page was quickly copied from the glimmer web site and readme file by Steffen Moeller moeller@debian.org for the Debian system. 💜

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aaaand that's the whole page! TIGR-GLIMMER (1) (1) — General Commands Manual, that's the source/version tag right there in the corner, no date on this one so don't come for me. mwah, go build your IMM, bestie. 💅✨🎀🦋🌸