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# $Id: FAQ,v 1.6 2002/03/08 20:36:25 jason Exp $
Bioperl FAQ
-----------
I. Bioperl in general
1. What is Bioperl?
2. Where do I go to get the latest release?
3. What is the difference between 0.9.x and 0.7.x? What do you mean
developer release?
4. Is it BioPerl, bioperl, bio.perl.org, Bioperl? What's the deal?
5. How do I figure out how to use a module?
6. I'm interested in the bleeding edge version of the code, where
can I get it?
7. Who uses this toolkit?
8. How should I cite Bioperl?
9. What are the License terms for Bioperl?
II. Sequences
1. How do I parse a sequence file?
2. I can't get sequences with Bio::DB::GenBank any more, why not?
3. How can I get NT_ or NM_ accessions from NCBI (Reference Sequences)?
III. Report parsing
1. I want to parse BLAST, how do I do this?
2. What's wrong with Bio::Tools::Blast?
3. I want to parse FastA, how do I do this?
4. Let's say I want to do pairwise alignments of 2 sequences how can
I do this?
IV. Utilities
1. How do I find all the ORFs in a nucleotide sequence? Antigenic sites
in a protein? Calculate nucleotide melting temperature? Find repeats?
2. How do I do motif searches with Bioperl? Can I do "find all sequences
that are 75% identical" to a given motif?
3. Can I query MEDLINE or other bibliographic repositories using Bioperl?
------------------------------------------------------------------------
This FAQ maintained by those listed below:
Jason Stajich <jason@bioperl.org>
Brian Osborne <b_i_osborne@hotmail.com>
------------------------------------------------------------------------
I. Bioperl in general
------------------------------------------------------------------------
1. What is Bioperl?
Bioperl is a tookit of perl modules useful in building
bioinformatics solutions in perl. It is built in an
object-oriented manner so that many modules depend on each other
to achieve a task. The collection of modules in the bioperl-live
repository consist of the core of the functionality of bioperl.
Additionally auxiliary modules for creating graphical interfaces
(bioperl-gui), persistent storage in RDMBS (bioperl-db), and
CORBA bridges to the BioCORBA (www.biocorba.org) specification
(bioperl-corba-server and bioperl-corba-client) are all available
as CVS modules in our repository.
2. Where do I go to get the latest release?
You can always get our releases from ftp://bioperl.org/pub/DIST.
Official releases will be noted on the website http://bioperl.org
3. What is the difference between 0.9.x and 0.7.x? What do you mean
developer release?
0.7.X series (0.7.0, 0.7.2) were all released in 2001 and were
stable releases on 0.7 branch. This means they had a set of
functionality that is maintained throughout (no experimental
modules) and were guaranteed to have all tests and subsequent bug
fix releases with the 0.7 designation would not have any API
changes.
The 0.9.X series was our first attempt at releasing so called
developer releases. These are snapshots of the actively
developed code that at a minimum pass all our tests
4. Is it BioPerl, bioperl, bio.perl.org, Bioperl? What's the deal?
Well, the perl.org guys granted us use of bio.perl.org. We
prefer to be called Bioperl or BioPerl (unlike our Biopython
friends). We're part of the Open Bioinformatics Foundation
(OBF) and so as part of the Bio{*} toolkits we prefer the
Bioperl spelling. But we're not really all that picky so no worries.
5. How do I figure out how to use a module?
Read the embedded perl documentation (Plain Old Documentation -
POD) that is part of every modules. Do
% perldoc MODULE
(careful - spelling and case counts!).
The bioperl tutorial - bptutorial.pl - provided in the root
directory of the bioperl release will also provide a good
introduction. There are links to tutorials off the bioperl
website that may provide some additional help.
There are also many scripts in the examples/ and scripts/
directories that could be useful - see bioperl.pod for a brief
description of all of them.
Additionally we have written many tests for our modules, you
can see test data and example usage of the modules in these
tests - look in the test dir (called 't').
6. I'm interested in the bleeding edge version of the code, where
can I get it?
Go to http://cvs.bioperl.org and you'll see instructions on how
to get the CVS code.
Basically:
% cvs -d :pserver:cvs@cvs.bioperl.org:/home/repository/bioperl login
enter 'cvs' for the password
% cvs -d :pserver:cvs@cvs.bioperl.org:/home/repository/bioperl
co bioperl_all
7. Who uses this toolkit?
Lots of people. Sanger Centre, EBI, many large and small
academic laboratories, large and small pharmaceutical companies.
All the developers on the bioperl list use the toolkit in some
capacity on a regular basis.
The Genquire annotation system (www.bioinformatics.org/Genquire/)
and Ensembl (www.ensembl.org) use bioperl as the basis for their
implementation.
8. How should I cite Bioperl?
For now cite it as "The Bioperl Project, http://www.bioperl.org".
9. What are the License terms for Bioperl?
Bioperl is licensed under the same terms as Perl itself which is
the Perl Artistic License. You can see more information on that
license at http://www.perl.com/pub/a/language/misc/Artistic.html
and http://www.opensource.org/licenses/artistic-license.html
------------------------------------------------------------------------
II. Sequences
------------------------------------------------------------------------
1. How do I parse a sequence file?
Use the Bio::SeqIO system. This will create Bio::Seq objects for
you. See the tutorial bptutorial.pl for more information or the
documentation for Bio::SeqIO (e.g. 'perldoc SeqIO.pm').
2. I can't get sequences with Bio::DB::GenBank any more, why not?
NCBI changed the web CGI script that provided this access. You
must be using bioperl <= 0.7.2. The developer release 0.9.3
contains this fix as does the 1.0 release.
3. How can I get NT_ or NM_ accessions from NCBI (Reference
Sequences)?
Use Bio::DB::RefSeq not Bio::DB::GenBank when you are retrieving
the NM_ accessions. This is still an area of active development
because the data providers have not provided the best interface
for us to query. EBI has provided a mirror with their dbfetch
system which is accessible through the Bio::DB::RefSeq object
however, there are cases where NT_ accessions will not be
retrievable.
------------------------------------------------------------------------
III. Report parsing
------------------------------------------------------------------------
1. I want to parse BLAST, how do I do this?
Well you might notice that there are a lot of choices. Sorry
about that. We've been evolving towards a single solution.
Currently the best way to parse a report is to use the SearchIO
system. This supports blast and fasta report parsing. The
bptutorial provides an example of how to use this system as well
as the documentation in the Bio::SearchIO system.
2. What's wrong with Bio::Tools::Blast?
Nothing is really wrong with it, it has just been outgrown by a
more generic approach to reports. This generic approach allows
us to just write pluggable modules for fasta and Blast parsing
while using the same framework. This is completely analogous to
the Bio::SeqIO system of parsing sequence files. However, the
objects produced are of the Bio::Search rather than Bio::Seq
variety.
3. I want to parse FastA or NCBI -m7 (XML) format, how do I do this?
It is as simple as parsing text BLAST results - you simply need
to specify the format as "fasta" or "blastxml" and the parser
will load the appropriate module for you. You can use the exact
logic and code for all of these formats as we have generalized
the modules for sequence database searching.
4. Let's say I want to do pairwise alignments of 2 sequences how can
I do this?
See the Bio::Factory::EMBOSS to see how to use the 'water' and
'needle' alignment programs that are part of the EMBOSS suite.
Additionally you can use the pSW module that is part of the
bioperl-ext package (distributed separated at
ftp://bioperl.org/pub/DIST). However note this only does protein
alignments and is no longer a supported module. Instead the
EMBOSS implementation is the the best path ahead unless someone
else wants to provide an Inline::C implementation.
------------------------------------------------------------------------
IV. Utilities
------------------------------------------------------------------------
1. How do I find all the ORFs in a nucleotide sequence? Antigenic sites
in a protein? Calculate nucleotide melting temperature? Find repeats?
In fact, none of these functions are built into Bioperl but they are
all available in the EMBOSS package (www.uk.embnet.org/Software/EMBOSS),
as well as many others. The Bioperl developers created a simple
interface to EMBOSS such that any and all EMBOSS programs can be run
from within Bioperl. See Bio::Factory::EMBOSS for more information.
If you can't find the functionality you want in Bioperl then make sure
to look for it in EMBOSS, these packages integrate quite gracefully
with Bioperl. Of course, you will have to install EMBOSS to get this
access.
2. How do I do motif searches with Bioperl? Can I do "find all sequences
that are 75% identical" to a given motif?
There are a number of approaches inside and outside of Bioperl. Within
Bioperl take a look at Bio::Tools::SeqPattern, but it's also conceivable
that the combination of Bioperl and Perl's regular expressions could do
the trick. You might also consider the CPAN module String::Approx (this
module addresses the percent match query). Or, take a look at the TFBS
package, at http://forkhead.cgb.ki.se/TFBS (Transcription Factor Binding
Site). This Bioperl-compliant package specializes in pattern searching
of nucleotide sequence using matrices.
3. Can I query MEDLINE or other bibliographic repositories using Bioperl?
Yes! The solution lies in Bio::Biblio*, a set of modules that provide
access to MEDLINE and OpenBQS-compliant servers using SOAP. See
Bio/Biblio.pm or examples/biblio.pl for details and example code.
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