TIGR-GLIMMER(1)

💖 TIGR-GLIMMER(1) — the girlies' guide to finding genes 💖

okay so. bestie. gather round. this is the manual page for tigr-glimmer, and it's genuinely one of the most iconic little gene-finders in the microbial world. let's get into it 💅

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✨ NAME ✨

tigr-glimmer — Find/Score potential genes in genome-file using the probability model in icm-file 🧬

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🌸 SYNOPSIS 🌸

tigr-glimmer3 [genome-file]  [icm-file]  [[options]]

that's it. that's the whole vibe check. two files and then whatever options you feel like serving ✨

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🦋 DESCRIPTION 🦋

so tigr-glimmer is a whole system for finding genes in microbial DNA — and like, specifically the genomes of bacteria and archaea. the name stands for Gene Locator and Interpolated Markov Modeler, which is a lot of words but basically: it uses interpolated Markov models (IMMs) to clock which regions are coding and which are just noncoding DNA chilling there doing nothing.

the IMM approach — described in the Nucleic Acids Research paper on tigr-glimmer 1.0 and in the follow-up paper on tigr-glimmer 2.0 — uses a combination of Markov models from 1st through 8th-order, and it weights each model according to its predictive power. and like, tigr-glimmer 1.0 and 2.0 use 3-periodic nonhomogenous Markov models in their IMMs. periodt.

tigr-glimmer is the primary microbial gene finder at TIGR, no cap, and it has been used to annotate the complete genomes of B. burgdorferi (Fraser et al., Nature, Dec. 1997), T. pallidum (Fraser et al., Science, July 1998), T. maritima, D. radiodurans, M. tuberculosis, and non-TIGR projects including C. trachomatis, C. pneumoniae, and others. its analyses of some of these genomes and others is available at the TIGR microbial database site. 👑

a special version of tigr-glimmer designed for small eukaryotes, GlimmerM, was used to find the genes in chromosome 2 of the malaria parasite, P. falciparum.. GlimmerM is described in S.L. Salzberg, M. Pertea, A.L. Delcher, M.J. Gardner, and H. Tettelin, "Interpolated Markov models for eukaryotic gene finding," Genomics 59 (1999), 24-31. click here (http://www.tigr.org/software/glimmerm/) to visit the GlimmerM site, which includes information on how to download the GlimmerM system. 🦋

the tigr-glimmer system consists of two main programs. the first of these is the training program, build-imm. this program takes an input set of sequences and builds and outputs the IMM for them. these sequences can be complete genes or just partial orfs. for a new genome, this training data can consist of those genes with strong database hits as well as very long open reading frames that are statistically almost certain to be genes. the second program is glimmer, which uses this IMM to identify putative genes in an entire genome. tigr-glimmer automatically resolves conflicts between most overlapping genes by choosing one of them. it also identifies genes that are suspected to truly overlap, and flags these for closer inspection by the user. these ``suspect'' gene candidates have been a very small percentage of the total for all the genomes analyzed thus far. tigr-glimmer is a program that... 👀

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🎀 OPTIONS 🎀

okay this is the part everyone actually scrolls to. every single flag, all of them, i'm not skipping a single one bestie 🫶

• -C n — use n as GC percentage of independent model.

note: n should be a percentage, e.g., -C 45.2 💜

• -f — use ribosome-binding energy to choose start codon.
• +f — use first codon in orf as start codon.
• -g n — set minimum gene length to n.
• -i filename — use filename to select regions of bases that are off limits, so that no bases within that area will be examined 🚫
• -l — assume linear rather than circular genome, i.e., no wraparound.
• -L filename — use filename to specify a list of orfs that should be scored separately, with no overlap rules.
• -M — input is a multifasta file of separate genes to be scored separately, with no overlap rules.
• -o n — set minimum overlap length to n. overlaps shorter than this are ignored.
• -p n — set minimum overlap percentage to n%. overlaps shorter than this percentage of *both* strings are ignored.
• -q n — set the maximum length orf that can be rejected because of the independent probability score column to (n - 1).
• -r — don't use independent probability score column.
• +r — use independent probability score column.
• -r — don't use independent probability score column.

not a typo bestie, the manual genuinely lists -r twice. i'm keeping it exactly as it is, character for character 💀

• -s s — use string s as the ribosome binding pattern to find start codons.
• +S — do use stricter independent intergenic model that doesn't give probabilities to in-frame stop codons. (option is obsolete since this is now the only behaviour)
• -t n — set threshold score for calling as gene to n. if the in-frame score >= n, then the region is given a number and considered a potential gene. 🔥
• -w n — use "weak" scores on tentative genes n or longer. weak scores ignore the independent probability score.

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🌈 SEE ALSO 🌈

the whole friend group, in order:

• tigr-adjust (1)
• tigr-anomaly (1)
• tigr-build-icm (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)
• tigr-glimmer3 (1)
• tigr-long-orfs (1)

also:

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

and fr fr, please see the readme in /usr/share/doc/glimmer for a description on how to use Glimmer. it's giving essential reading 📖

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🧚 AUTHOR 🧚

this manual page was quickly copied from the glimmer web site by Steffen Moeller moeller@debian.org for the Debian system. ty for your service king 🫡

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and that's the whole page bestie!! this lil manual lives in the General Commands Manual and signs off as TIGR-GLIMMER(1) — so go find some genes, slay, and remember: every flag here is real, even the duplicated one 💖✨🎀🦋🌸💅