GTH(1)

💖 GTH(1) — the manual, but make it cute 💖

okay bestie, welcome to GTH(1), which is literally the manual page for the one and only gth. Section 1, we love a classic. Sit down, grab a strawberry 🍓, and let's get into it.

---

✨ NAME ✨

gth — predict genome structures 🧬

---

🌸 SYNOPSIS 🌸

gth [option ...] -genomic file [...] -cdna file [...] -protein file
[...]

---

🦋 DESCRIPTION 🦋

So basically it computes similarity-based gene structure predictions — a.k.a. spliced alignments — using cDNA/EST and/or protein sequences, and then it assembles all those resulting spliced alignments into consensus spliced alignments. It's giving glow-up for your sequences. 💅

---

👑 OPTIONS 👑

There are... a lot. Not me counting them. But we do all of them, no skips, periodt. 🎀

• -genomic <file> — specify input files containing genomic sequences. This one is mandatory, bestie, you literally cannot skip it.
• -cdna <file> — specify input files containing cDNA/EST sequences.
• -protein <file> — specify input files containing protein sequences.
• -species <species> — specify species to select the splice site model which is most appropriate. Possible species: "human" "mouse" "rat" "chicken" "drosophila" "nematode" "fission_yeast" "aspergillus" "arabidopsis" "maize" "rice" "medicago". default: undefined
• -bssm — read bssm parameter from a file in the path given by the environment variable BSSMDIR. default: undefined
• -scorematrix — read the amino acid substitution scoring matrix from a file in the path given by the environment variable GTHDATADIR. default: BLOSUM62
• -translationtable — set the codon translation table used for codon translation in matching, DP, and output. default: 1
• -f — analyze only the forward strand of genomic sequences. default: no
• -r — analyze only the reverse strand of genomic sequences. default: no
• -cdnaforward — align only the forward strand of cDNAs. default: no
• -frompos — analyze genomic sequence from this position. requires -topos or -width; counting from 1 on. default: 0
• -topos — analyze genomic sequence to this position. requires -frompos; counting from 1 on. default: 0
• -width — analyze only this width of genomic sequence. requires -frompos. default: 0
• -v — be verbose. default: no
• -xmlout — show output in XML format. default: no
• -gff3out — show output in GFF3 format. default: no
• -md5ids — show MD5 fingerprints as sequence IDs. default: no
• -o — redirect output to specified file. default: undefined
• -gzip — write gzip compressed output file. default: no
• -bzip2 — write bzip2 compressed output file. default: no
• -force — force writing to output file. default: no
• -skipalignmentout — skip output of spliced alignments. default: no
• -mincutoffs — show full spliced alignments, i.e., cutoffs mode for leading and terminal bases is MINIMAL. default: no
• -showintronmaxlen — set the maximum length of a fully shown intron. If set to 0, all introns are shown completely. default: 120
• -minorflen — set the minimum length of an ORF to be shown. default: 64
• -startcodon — require than an ORF must begin with a start codon. default: no
• -finalstopcodon — require that the final ORF must end with a stop codon. default: no
• -showseqnums — show sequence numbers in output. default: no
• -pglgentemplate — show genomic template in PGL lines (switch off for backward compatibility). default: yes
• -gs2out — output in old GeneSeqer2 format. default: no
• -maskpolyatails — mask poly(A) tails in cDNA/EST files. default: no
• -proteinsmap — specify smap file used for protein files. default: protein
• -noautoindex — do not create indices automatically except for the .dna.* files used for the DP. existence is not tested before an index is actually used! default: no
• -createindicesonly — stop program flow after the indices have been created. default: no
• -skipindexcheck — skip index check (in preprocessing phase). default: no
• -minmatchlen — specify minimum match length (cDNA matching). default: 20
• -seedlength — specify the seed length (cDNA matching). default: 18
• -exdrop — specify the Xdrop value for edit distance extension (cDNA matching). default: 2
• -prminmatchlen — specify minimum match length (protein matches). default: 24
• -prseedlength — specify seed length (protein matching). default: 10
• -prhdist — specify Hamming distance (protein matching). default: 4
• -online — run the similarity filter online without using the complete index (increases runtime). default: no
• -inverse — invert query and index in vmatch call. default: no
• -exact — use exact matches in the similarity filter. default: no
• -gcmaxgapwidth — set the maximum gap width for global chains. defines approximately the maximum intron length. set to 0 to allow for unlimited length. in order to avoid false-positive exons (lonely exons) at the sequence ends, it is very important to set this parameter appropriately! default: 1000000
• -gcmincoverage — set the minimum coverage of global chains regarding to the reference sequence. default: 50
• -paralogs — compute paralogous genes (different chaining procedure). default: no
• -enrichchains — enrich genomic sequence part of global chains with additional matches. default: no
• -introncutout — enable the intron cutout technique. default: no
• -fastdp — use jump table to increase speed of DP calculation. default: no
• -autointroncutout — set the automatic intron cutout matrix size in megabytes and enable the automatic intron cutout technique. default: 0
• -icinitialdelta — set the initial delta used for intron cutouts. default: 50
• -iciterations — set the number of intron cutout iterations. default: 2
• -icdeltaincrease — set the delta increase during every iteration. default: 50
• -icminremintronlen — set the minimum remaining intron length for an intron to be cut out. default: 10
• -nou12intronmodel — disable the U12-type intron model. default: no
• -u12donorprob — set the probability for perfect U12-type donor sites. default: 0.99
• -u12donorprob1mism — set the prob. for U12-type donor w. 1 mismatch. default: 0.90
• -probies — set the initial exon state probability. default: 0.50
• -probdelgen — set the genomic sequence deletion probability. default: 0.03
• -identityweight — set the pairs of identical characters weight. default: 2.00
• -mismatchweight — set the weight for mismatching characters. default: -2.00
• -undetcharweight — set the weight for undetermined characters. default: 0.00
• -deletionweight — set the weight for deletions. default: -5.00
• -dpminexonlen — set the minimum exon length for the DP. default: 5
• -dpminintronlen — set the minimum intron length for the DP. default: 50
• -shortexonpenal — set the short exon penalty. default: 100.00
• -shortintronpenal — set the short intron penalty. default: 100.00
• -wzerotransition — set the zero transition weights window size. default: 80
• -wdecreasedoutput — set the decreased output weights window size. default: 80
• -leadcutoffsmode — set the cutoffs mode for leading bases. can be either RELAXED, STRICT, or MINIMAL. default: RELAXED
• -termcutoffsmode — set the cutoffs mode for terminal bases. can be either RELAXED, STRICT, or MINIMAL. default: STRICT
• -cutoffsminexonlen — set the cutoffs minimum exon length. default: 5
• -scoreminexonlen — set the score minimum exon length. default: 50
• -minaveragessp — set the minimum average splice site prob. default: 0.50
• -duplicatecheck — criterion used to check for spliced alignment duplicates, choose from none|id|desc|seq|both. default: both
• -minalignmentscore — set the minimum alignment score for spliced alignments to be included into the set of spliced alignments. default: 0.00
• -maxalignmentscore — set the maximum alignment score for spliced alignments to be included into the set of spliced alignments. default: 1.00
• -mincoverage — set the minimum coverage for spliced alignments to be included into the set of spliced alignments. default: 0.00
• -maxcoverage — set the maximum coverage for spliced alignments to be included into the set of spliced alignments. default: 9999.99
• -intermediate — stop after calculation of spliced alignments and output results in reusable XML format. Do not process this output yourself, use the ``normal'' XML output instead! default: no
• -sortags — sort alternative gene structures according to the weighted mean of the average exon score and the average splice site probability. default: no
• -sortagswf — set the weight factor for the sorting of AGSs. default: 1.00
• -exondistri — show the exon length distribution. default: no
• -introndistri — show the intron length distribution. default: no
• -refseqcovdistri — show the reference sequence coverage distribution. default: no
• -first — set the maximum number of spliced alignments per genomic DNA input. Set to 0 for unlimited number. default: 0
• -help — display help for basic options and exit.
• -help+ — display help for all options and exit.
• -version — display version information and exit.

---

🌈 that's the whole vibe 🌈

Heads up bestie: -genomic <file> is mandatory, and pleaseeee read the -gcmaxgapwidth and -noautoindex notes again before you run something wild. 🫶

And that's a wrap on the GTH(1) page, fr fr. This was the manual page GTH(1) — that's the title and the manual name right there, we love a matching set 💖 — and the footer says GTH(1) too, so the whole thing is just iconic bookends. Go predict some genome structures, main character. 😭👑