Bug 254027 – [science] new package sci-biology/estscan: ESTScan can detect coding regions in DNA/RNA sequences, even if they are of low quality (e.g. EST sequences). ESTScan will also detect and correct sequencing errors that lead to frameshifts

• Status: CONFIRMED
• Product: Gentoo Linux

[Description Martin Mokrejš 2009-01-07 00:14:07 UTC]

This is another very useful package.

[Comment 1 Martin Mokrejš 2009-01-07 00:16:39 UTC]

Created attachment 177615 [details]
estscan-3.0.2.ebuild

Working ebuild.

[Comment 2 Andrey Kislyuk (RETIRED) 2009-03-19 17:15:55 UTC]

The package looks pretty serious, but its premise seems very tenuous to me. Essentially, it tries to distinguish UTRs from CDS in EST sequences de novo, is that right? It doesn't use genome sequence information or comparative information for this task. It also tries to correct sequencing errors in ESTs, which only seems useful if you don't have the genome.

This strikes me as very limited in application. What do you think, Martin?

[Comment 3 Martin Mokrejš 2009-03-19 19:11:29 UTC]

This is one of the few applications which can cluster ESTs while trying to come
over the sequencing errors while utilizing CDS knowledge. Yes, it might appear obsolete but not that many genomes are sequenced yet. It is nevertheless probably best choice for those working with ESTs of genomes still not known.

[Comment 4 Martin Mokrejš 2011-02-14 18:13:48 UTC]

I placed a 3.0.3 ebuild into the science overlay. Due to my blindness there is some QA issue with its IUSE line. Few more lines need more cleanup (see comments in the ebuild). Other than that, it works.

This is ESTscan3, something older on sourceforge is ESTscan1 and ESTscan2. ESTscan is still useful package, really.