Download kPerl kPerl-2.07.zip now;
Blast.pl BLAST wrapper
Gap.pl wrapper to Staden's GAP4 package
GscjGap.pl more locale-specific utilities Staden's GAP4 package
Net.pl internet-based utilities
Plot.pl generate plot diagrams using the GD package
SeqHandle.pl basic sequence utilities: formatting, selection etc.
SeqMotif.pl sequence motif analysis
A detailed description for the frontend scripts of the package can be found
in the package subdirectory DocExample/.
To install the package and adjust it to your enviroment
(1) extract the package into an appropriate path, e.g.
(2) add the package path (e.g. /usr/local/src/kPerl) to
the environment variable $PERL5LIB or define an extra
environment variable $KPERLPATH .
It may also be useful to add the package path to
environment variable $PATH .
(3) install necessary CPAN modules that are listed in the
package's file DocExample/ExternalDependencies.txt .
(4) adjusts path definitions in the package's module
MainLib/Path.pm . This module works as an interface
to external software.
Perl packages (CPAN) that are used throughout this suite. You will need to
install these using cpan or cpanplus.
essentially required by SeqLab::SeqStreamIn, preferably used by
MainLib::Data, accounted for in SeqLab::SeqFormat
WARNING: previous version 0.14 had a serious bug concerning
method tell() which would cause fatals in SeqLab::SeqFormat.
WARNING: versions 0.15, 0.16 (and previous?) won't install
to certain environments, unless newest Scalar::Util is
installed explicitly (CPAN won't recognise the dependency).
And note that perl requires an API patch to support WeakRefs.
successfully used $FileHandle::Unget::VERSION 1.5, 1.6 [2004-09-12 SuSE 9.0]
successfully used $FileHandle::Unget::VERSION 1.621 [2005-04-25 SuSE 9.2]
GD specific use of gdlib >= v1.20 (PNG support)
The current package requires gdlib >= 2.0.12, including the
LWP::UserAgent limited use in Net.pl
now included in perl distribution, at least since 5.10.0
successfully used $LWP::UserAgent::VERSION 2.001
successfully used $LWP::UserAgent::VERSION 2.024 [2005-04-25 SuSE 9.2]
Math::Round quite useful
MemHandle currently used in SeqLab::SeqFormat (output filter "struct")
and SeqAlign::AlnProj (function &AlnprojParamSprint). Usage of
this module may be scattered even more in the future.
MIME::Parser limited use in Net.pl
part of MIME-tools
MIME::Parser depends on several other packages
tried $MIME::Parser::VERSION 5.406, 2000-11-12
Binaries that are used in / wrapped through this suite and that are available
from the author.
nblock fast processing of NNN joints in nucleotide sequences, esp.
program function "-f split"
RunPWMnt ) obsolete, former version of PWMscanNt (pwmsuite)
RunPWMprot ) obsolete, former version of PWMscanAa (pwmsuite)
Binaries that are used in / wrapped through this suite, while they are not part
of the distribution.
mmencode MIME coding/decoding
part of the metamail program package
it may be replaced by any other program or bunch of programs
that allows coding/uncoding of MIME types