EST2GENOME(1e)

💖 EST2GENOME 💖

ok so this is the est2genome manual page, from the EMBOSS Manual for Debian, and bestie I am so ready to tell you about it 🧚

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✨ NAME ✨

est2genome — align EST sequences to genomic DNA sequence. that's it, that's the whole vibe. your little EST gets matched up against a whole genome and honestly? iconic behavior 💅

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🌸 SYNOPSIS 🌸

est2genome -estsequence seqall -genomesequence sequence [-match integer]
           [-mismatch integer] [-gappenalty integer]
           [-intronpenalty integer] [-splicepenalty integer]
           [-minscore integer] -reverse boolean -usesplice boolean
           -mode list -best boolean -space float -shuffle integer
           -seed integer -outfile outfile -align boolean -width integer

est2genome -help

notice how the first chunk is mandatory (no brackets, no escape) and everything in square brackets is optional. the way the required args just are required? periodt.

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🦋 DESCRIPTION 🦋

est2genome is a command line program from EMBOSS, aka "the European Molecular Biology Open Software Suite" — say that five times fast, I dare you 😭

it lives in the "Alignment:Global" command group(s). so if you're browsing the group chat of alignment tools, this is where she hangs out. no cap.

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👑 OPTIONS 👑

🎀 Input section

• -estsequence seqall — the EST sequence(s) you're feeding in 💖
• -genomesequence sequence — the genomic sequence it's getting aligned against 🌸

🌈 Additional section

• -match integer — Default value: 1
• -mismatch integer — Default value: 1
• -gappenalty integer — cost for deleting a single base in either sequence, excluding introns. Default value: 2
• -intronpenalty integer — cost for an intron, independent of length. Default value: 40
• -splicepenalty integer — cost for an intron, independent of length and starting/ending on donor-acceptor sites. Default value: 20
• -minscore integer — exclude alignments with scores below this threshold score, like a bouncer at the club door 💅. Default value: 30

🧚 Advanced section

• -reverse boolean — reverse the orientation of the EST sequence. flips it, no biggie.
• -usesplice boolean — use donor and acceptor splice sites. if you want to ignore donor-acceptor sites then set this to be false. Default value: Y
• -mode list — this determines the comparison mode. the default value is 'both', in which case both strands of the est are compared assuming a forward gene direction (ie GT/AG splice sites), and the best comparison redone assuming a reversed (CT/AC) gene splicing direction. the other allowed modes are 'forward', when just the forward strand is searched, and 'reverse', ditto for the reverse strand. Default value: both
• -best boolean — you can print out all comparisons instead of just the best one by setting this to be false. Default value: Y
• -space float — for linear-space recursion. if product of sequence lengths divided by 4 exceeds this then a divide-and-conquer strategy is used to control the memory requirements. in this way very long sequences can be aligned. if you have a machine with plenty of memory you can raise this parameter (but do not exceed the machine's physical RAM 😭). Default value: 10.0
• -shuffle integer — (no default listed, she's mysterious like that 🙈)
• -seed integer — Default value: 20825

🍓 Output section

• -outfile outfile — where the output goes 💖
• -align boolean — show the alignment. the alignment includes the first and last 5 bases of each intron, together with the intron width. the direction of splicing is indicated by angle brackets (forward or reverse) or ???? (unknown).
• -width integer — Default value: 50

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💀 BUGS 💀

bugs can be reported to the Debian Bug Tracking system (http://bugs.debian.org/emboss), or directly to the EMBOSS developers (http://sourceforge.net/tracker/?group_id=93650&atid=605031).

if you find a bug, don't be shy, tell them. they want to know. fr fr 🫶

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⭐ SEE ALSO ⭐

est2genome is fully documented via the tfm(1) system. go read that too, bestie, it's giving ✨thorough✨.

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💜 AUTHOR 💜

Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>

• wrote the script used to autogenerate this manual page. so yes, a script wrote the original of what you're reading right now, and I rewrote it with feelings. the circle of life 🌈

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🌸 COPYRIGHT 🌸

this manual page was autogenerated from an Ajax Control Definition of the EMBOSS package. it can be redistributed under the same terms as EMBOSS itself.

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heads up bestie: the -space warning is real — do not push that number past your machine's physical RAM. she will not survive it 💀

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and that's the whole page!! this was EMBOSS 6.4.0, dated 05/11/2012, and it was EST2GENOME(1e) the entire time 🎀 thanks for reading, mwah 💖