[Bioperl-l] Fw: perly suffix trees--

[Aaron Mackey]

Fair enough, thanks!

FYI, I've used one of Ian Korf's other clever tricks in my own code before:
using six different intron states (combined with 3 exon states that
correspond to the previous intron's phase) in a gene-model HMM to ensure
that spliced codons don't encode stop codons.  I'm not aware of any other
gene finder that implements that structure directly (my impression is that
these cases are disallowed through some *post hoc* checking).

-Aaron

On Thu, Jul 16, 2009 at 8:48 AM, Mark A. Jensen <maj at fortinbras.us> wrote:

> To the list with you, I have no secrets-- maybe Ian will chime in.
> cheers,
> MAJ
> ----- Original Message -----
> From: Aaron Mackey
> To: Mark A. Jensen
> Sent: Thursday, July 16, 2009 8:41 AM
> Subject: Re: [Bioperl-l] perly suffix trees--
>
>
> The code on that wiki page looks suspiciously incomplete.  For example, you
> declare $i = 0 in readDictionary, then never use it again.  It also looks
> like you only ever create entries for the entire word, and never any
> suffices (which presumably was what the $i was going to be for, to offset
> into each word).
>
> Further, it looks like the readDictionary loop will clobber already-seen
> fragments by reassigning "1" (when they might already be the prefix to some
> other suffix).  Perhaps the missing $i loop would reveal to me how this
> would be avoided.
>
> It also seems like testing for a hashref to equal 1 during the search is
> asking for type mismatch trouble; perhaps better to directly test the ref()
> status to determine rightmost/inner status? But that's just style, not
> substance.
>
> Best wishes,
>
> -Aaron
>
>
> On Mon, Jul 13, 2009 at 10:15 PM, Mark A. Jensen <maj at fortinbras.us>
> wrote:
>
>  Hi All-
>  Russell sent me an almost magical Perl algorithm for creating a suffix
> tree
>  or something like one. It was cool enough to make a scrap out of it--
>  http://www.bioperl.org/wiki/Suffix_trees_from_thin_air
>  Have a look; might be diverting-
>  cheers
>  Mark
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