Re: HLA (A,B,C,Dr,DQ) typing via sequence software

Peter Claussen wrote:

> In article <pt-dnZj3KJo0kRHcRVn-tQ@[EMAIL PROTECTED]
>,
>  Fetch-Rover-Fetch@[EMAIL PROTECTED]
 wrote:
> 
> 
>>anyone know of *any* commercial, shareware, or freeware software to do 
>>this task??  Mac or Pc
>>
>>
>>the software that has been presented to us as the *only* alternative 
>>(called 'Assign') from a company in Australia is fubar.
>>
>>the licensing requires a separate license for **EACH USER** on a single 
>>machine.  Requires the a 'hardware id' be sent to au to get lic key.
>>
>>It took over a week to get the lic key the first time.
>>
>>the "projects" do not im****t data into some database, rather they track 
>>the original data file's (.abi format) directory path.  If the data file

>>is moved the project n longer works as it can not find the file and does

>>not give an option to locate it.
>>
>>who the hell knows if it actually does its job!!!
>>
>>any help, links places to start looking etc is welcome
>>
>>Thanks in advance
> 
> 
> If I understand the question, then you're looking for something 
> like the software ****tion of this:
>
http://www4.amershambiosciences.com/aptrix/upp01077.nsf/Content/150294ABE
> BB84061C1256BEC003020E3/$FILE/HLAtyp.pdf
> 
> This sounds like the complete package, reagents and all - but you're
> question sounds like just the sequence analysis - how are you generating
> sequence data? (I'm a bit out of touch with current state of sequencing 
> hardware, but I assume *.abi is the generated data).
> 
> Peter Claussen
Sorry if I was not clear enough to start.

the sequence data is being generated by an ABI model 3730 capillary 
sequencer.  The resulting data file (the actual sequence information) is 
placed is a file with the extension ".abi", and programs like Sequencher 
and Vector NTI read these and display cromatagraphs, and can also 
sequence alignment (to other sequences).  BUT these programs do not 
"type" - make a determination of the HLA alleles found in the sample.

This is what I need the software I am looking for to do; HLA typing from 
the raw sequence data.  The software (as I initially stated) that ABI 
(Applied Bio Systems) is trying to force on us for this purpose - is 
unstable, has an extremely onerous licensing implementation, and seems 
to be unable to deal with data files that have been moved from the 
location where they were initially "im****ted" (their terminology).

Again, Thanks for any help.

BTW - the abi link above may break as I get a page saying they (abi) are 
updating their web site.  Is "APPTRIX" the name of the software?
thanks