[Bioperl-l] Feature table comparison

[Sean Davis]

Rob,

If you have files in EMBL format, you can use Bio::SeqIO to read them.  
What is in the EMBL files--protein or DNA?  Are the features named in a 
systematic manner (are the same genes called the same thing in both 
strains if they are present)?  If they are, can you simply do an ID 
matching between the two strains?  Judging from your email below, 
probably not.

If the question you are asking is truly the opposite of an alignment, 
then you will need to do more work.  This is beyond my usual 
bioinformatics realm, but I would imagine that you would need to align 
the two genomes first (and how you do this will greatly affect your 
results, I would suppose) and then look for what didn't align in each 
strain.  I'm sure others on the list have done this kind of thing 
before.  I'm just not sure what the state-of-the-art is for 
whole-genome alignments these days.

Sean

On Jan 18, 2005, at 4:36 AM, Robert Minshall wrote:

> i am basically trying to find the differences between 2 strains of 
> bacteria in
> embl format. what i really need is an inverted ACT (Artemis comparison 
> tool)
> diffseq from emboss wont do what i need, i just need to some how get a 
> list of
> protiens that are on one strain and not the other. This cn be done by 
> hand but
> will take months. oi was woundereing if there was a program out there 
> where i
> can input the 2 embl files and get a list of feature differences or the
> opposite of an alignment.
> Thanks
> Rob
> --
> Robert J Minshall
> Postgraduate Researcher in Microbiology,
> Biosciences Research Institute,
> School of Environment and Life Sciences,
> Lab 209 Cockcroft Building,
> University of Salford,
> Salford,
> Greater Manchester.
> M5 4WT
> UK
> 0161 2952652
> r.j.mishall at pgr.salford.ac.uk
>
>
>
> Quoting Sean Davis <sdavis2 at mail.nih.gov>:
>
>> Rob,
>>
>> You will probably need to be a bit more specific.  What constitutes a
>> "genome" in your email below?  What are the features?  In what form 
>> are you
>> getting the data?  Do you have a specific question you are trying to 
>> answer?
>>
>> Sean
>>
>> ----- Original Message -----
>> From: "Robert Minshall" <R.J.Minshall at pgr.salford.ac.uk>
>> To: <bioperl-l at bioperl.org>
>> Sent: Monday, January 17, 2005 8:39 AM
>> Subject: [Bioperl-l] Feature table comparison
>>
>>
>>>
>>> Hi does any one know of or have a script that can compare the faeture
>>> tables of
>>> genomes and show what appears on one and not the other. ie i want to 
>>> find
>>> the
>>> differenmces on the feature tables. is this possible i'm new to perl 
>>> and
>>> was
>>> hoping that someone could point me in the right direction. my email 
>>> is
>>> r.j.minshall at pgr.salford.ac.uk
>>> thanks in advance
>>> Rob Minshall
>>>
>>> --
>>> Robert J Minshall
>>> Postgraduate Researcher in Microbiology,
>>> Biosciences Research Institute,
>>> School of Environment and Life Sciences,
>>> Lab 209 Cockcroft Building,
>>> University of Salford,
>>> Salford,
>>> Greater Manchester.
>>> M5 4WT
>>> UK
>>> 0161 2952652
>>> r.j.mishall at pgr.salford.ac.uk
>>>
>>>
>>>
>>>
>>>
>>>
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>>
>>
>>
>
>
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