[Bioperl-l] [ANNOUCEMENT] BioPerl 1.6 RC3

Martin MOKREJŠ mmokrejs at ribosome.natur.cuni.cz
Sat Feb 21 16:31:46 EST 2009

For the completeness of the archives, it seems there used to
be a Gelminder tool to read gel files.
I cannot find anymore other sources than a backup of RCS files.
But somebody more skilled is probably able to recreate the
sources from the RCS-generated diffs.


For sure that should be helpful to somebody having the time
to read in the sources how to interpret the file format.
Not my case, though. ;)

Phillip San Miguel wrote:
> Okay, here are bunch of them:
> http://www.genomics.purdue.edu/~pmiguel/technical/alx/
> (Had them on a zip disk...)
> phred no longer appears to be able to read them.
> Chris Fields wrote:
>> Might be worth a try if you can dig any files up.  Frankly if it
>> doesn't work we can probably deprecate that module, unless someone out
>> there managed to get it working.
>> chris
>> On Jan 21, 2009, at 6:45 AM, Phillip San Miguel wrote:
>>>   And the late 90's!
>>>   The situation is a little more complex though. Pharmacia had an
>>> older instrument or two called the "Alf" and/or "Alf-red". I never
>>> saw one of those. But the Alfx -- that instrument rocked my world!
>>> 700+ base reads were common and there was a cycle sequencing kit
>>> available so I could sequence off 25+ kb subclones and lambda DNA.
>>>   Anyway, I can probably dig up some .alx files. But I think I tried
>>> to read one with SeqIO once and it failed. So it may be that
>>> Bio::SeqIO::alf really only reads the older .alf files, not the more
>>> modern .alx trace file format.
>>>   Phred could read them--poorly. It used the raw, rather than the
>>> processed traces, evidently.
>>> Phillip
>>> Brian Osborne wrote:
>>>> Chris,
>>>> This is my doing. Way back when I made an individual test file for
>>>> each SeqIO module, then did my best to find example files for each
>>>> format. I never did find an ALF output file, these machines were
>>>> used in the early '90's.
>>>> Brian O.
>>>> On Jan 18, 2009, at 12:07 AM, Chris Fields wrote:
>>>>> For some reason we have a test suite for Bio::SeqIO::alf but
>>>>> apparently no test data!

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