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 import 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

In article <pt-dnZj3KJo0kRHcRVn-tQ@britsys.net>,
Fetch-Rover-Fetch@K9University.edu 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 import 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

Err.. what kind of software are you actually looking for? You kind of
need to say what you need the software to do before people can suggest
likely choices.

--
Tom "Tom" Harrington
Macaroni, Automated System Maintenance for Mac OS X.
Version 2.0: Delocalize, Repair Permissions, lots more.
See http://www.atomicbird.com/

Tom Harrington <tph@pcisys.no.spam.dammit.net> wrote:

> In article <pt-dnZj3KJo0kRHcRVn-tQ@britsys.net>,
> Fetch-Rover-Fetch@K9University.edu 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 import 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
>
> Err.. what kind of software are you actually looking for? You kind of
> need to say what you need the software to do before people can suggest
> likely choices.

Err.. read the title of the post...


--
Johan W. Elzenga johan<<at>>johanfoto.nl
Editor / Photographer http://www.johanfoto.nl/

In article <pt-dnZj3KJo0kRHcRVn-tQ@britsys.net>,
Fetch-Rover-Fetch@K9University.edu 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 import 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 portion of this:
http://www4.amershambiosciences.com/...tent/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

Peter Claussen wrote:

> In article <pt-dnZj3KJo0kRHcRVn-tQ@britsys.net>,
> Fetch-Rover-Fetch@K9University.edu 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 import 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 portion of this:
> http://www4.amershambiosciences.com/...tent/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 "imported" (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

In article <1gmt1l3.1p9pmrpnah14yN%nomail@please.invalid>,
nomail@please.invalid (Johan W. Elzenga) wrote:

> Tom Harrington <tph@pcisys.no.spam.dammit.net> wrote:
>
> > In article <pt-dnZj3KJo0kRHcRVn-tQ@britsys.net>,
> > Fetch-Rover-Fetch@K9University.edu 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 import 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
> >
> > Err.. what kind of software are you actually looking for? You kind of
> > need to say what you need the software to do before people can suggest
> > likely choices.
>
> Err.. read the title of the post...

OK, in that case it's just a matter of translating the requirements into
something vaguely approaching English...

--
Tom "Tom" Harrington
Macaroni, Automated System Maintenance for Mac OS X.
Version 2.0: Delocalize, Repair Permissions, lots more.
See http://www.atomicbird.com/

Tom Harrington <tph@pcisys.no.spam.dammit.net> wrote:

> > > Err.. what kind of software are you actually looking for? You kind of
> > > need to say what you need the software to do before people can suggest
> > > likely choices.
> >
> > Err.. read the title of the post...
>
> OK, in that case it's just a matter of translating the requirements into
> something vaguely approaching English...

If you don't know what 'HLA (A,B,C,Dr,DQ) typing via sequence' is, still
doesn't mean it's not English. People who know about this kind of
molecular biology software certainly do understand the question.


--
Johan W. Elzenga johan<<at>>johanfoto.nl
Editor / Photographer http://www.johanfoto.nl/

In article <jsmdnU5wN648TxHcRVn-jw@britsys.net>,
Fetch-Rover-Fetch@K9University.edu wrote:

> Peter Claussen wrote:
>
> > In article <pt-dnZj3KJo0kRHcRVn-tQ@britsys.net>,
> > Fetch-Rover-Fetch@K9University.edu 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 import 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 portion of this:
> > http://www4.amershambiosciences.com/...tent/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 "imported" (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

If you simply want a ABI trace viewer then:
<http://www.geospiza.com/finchtv/down.../FinchTV_1_2_0
..dmg>

It seems to work on the traces that I have (though it doesn't do
alignments which makes it useless for me).

--
P. A.

<Fetch-Rover-Fetch@K9University.edu> wrote:

> anyone know of *any* commercial, shareware, or freeware software to do
> this task?? Mac or Pc

Not off the top of my head, but I do know a genetic programming[1]
expert who has had considerable success at creating custom search and
sequencing algorithms for commercial use. If you are interested I could
put him and you in touch.




[1] That's as in GP the computer science, not just programming related
to genetics.
--
"They that can give up essential liberty to obtain a little
temporary safety deserve neither liberty nor safety."

-- Benjamin Franklin, 1759

In article <jsmdnU5wN648TxHcRVn-jw@britsys.net>,
Fetch-Rover-Fetch@K9University.edu wrote:

> Peter Claussen wrote:
>
> > In article <pt-dnZj3KJo0kRHcRVn-tQ@britsys.net>,
> > Fetch-Rover-Fetch@K9University.edu 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 import 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 portion of this:
> > http://www4.amershambiosciences.com/...tent/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 clarifies the problem significantly.

> 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 "imported" (their terminology).
>

Software that would generate a listing of HLA alleles from DNA sequence
data sounds to be pretty specialized; more so since you talk of
"projects", which I would suspect (without having used the software) is
specific to the ABI product.

You may be able to replicate the workflow using other tools, but it may
not be as clean as you'd like. As you say, Sequencher, and others, can
read and align chromatographs. To make type determination, don't you
simply need to align an unknown DNA sequence to a known HLA allele?

So all you really need is a database of known HLA alleles, and then use
third party software to align your unknown sequences to find the best
match within that database.

That, at least, is how the process sounds to me.

There are several tools available for searching for best sequences
matches within a database, but these tools would not be specialized for
HLA typing, so you may not gain much in ease of use.

There might be packages that could be adapted to your needs, but I
couldn't say - I've toyed with a few of the packages available (as part
of teaching biology) but haven't done any real work. Off the top of my
head, a good source would be http://bioteam.net/MacOSX/.

After a little more poking around, I found
http://genome.ucsc.edu/bestlinks.html

This linked to http://imgt.cines.fr/ - then to (under "IMGT/V-QUEST
(sequence alignment software for IG, TR and HLA)")

http://www.ebi.ac.uk/imgt/hla/dnaplot.html

which may be closer to your problem.

Peter Claussen

> 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

The site doesn't name the package, just gives a general description.

As an aside, I can understand your frustration. When I was grad student,
I was forced to use software the controlled HPLC - software that was a
good example of poor design. Very non-standard interface - a thing I try
to avoid as a programmer.

Peter Claussen

Peter Claussen wrote:
THANKS!

thse should help me get started in finding what I am looking for.

Peter Claussen wrote:
> In article <pt-dnZj3KJo0kRHcRVn-tQ@britsys.net>,
> Fetch-Rover-Fetch@K9University.edu wrote:
>>anyone know of *any* commercial, shareware, or freeware software to do
>>this task?? Mac or Pc
> If I understand the question, then you're looking for something
> like the software portion of this:
> http://www4.amershambiosciences.com/...tent/150294ABE
> BB84061C1256BEC003020E3/$FILE/HLAtyp.pdf
>

There are several trace file readers including 4Peaks, which give raw
sequence.
From there, the alignment can be done quite easily with BioPerl or
SequenceAnalysis (see apple site- scientific dowloads).

Cheers.

wheat wrote:

> Peter Claussen wrote:
>
>> In article <pt-dnZj3KJo0kRHcRVn-tQ@britsys.net>,
>> Fetch-Rover-Fetch@K9University.edu wrote:
>>
>>> anyone know of *any* commercial, shareware, or freeware software to
>>> do this task?? Mac or Pc
>>
>> If I understand the question, then you're looking for something like
>> the software portion of this:
>> http://www4.amershambiosciences.com/...tent/150294ABE
>> BB84061C1256BEC003020E3/$FILE/HLAtyp.pdf
>>
>
> There are several trace file readers including 4Peaks, which give raw
> sequence.
> From there, the alignment can be done quite easily with BioPerl or
> SequenceAnalysis (see apple site- scientific dowloads).
>
> Cheers.
Thanks!