Seq

Bio::Seq is a sequence object, with features. SYNOPSIS # This is the main sequence object in Bioperl # gets a sequence from a file $seqio = Bio::SeqIO->new( -format => embl , -file => myfile.dat); $seqobj = $seqio->next_seq(); # SeqIO can both read and write sequences; see Bio::SeqIO #... Platforms: *nix

ALEXA-Seq is a method for using massively parallel paired-end transcriptome sequencing for 'alternative expression analysis'. Features . Alternative expression analysis . WTSS/RNA-Seq library quality assessment . Gene expression analysis . Novel transcript discovery . Visualization of... Platforms: *nix

Bio::Graphics::Panel is a Perl module to generate GD images of Bio::Seq objects. SYNOPSIS # This script parses a GenBank or EMBL file named on the command # line and produces a PNG rendering of it. Call it like this: # render.pl my_file.embl | display - use strict; use Bio::Graphics;... Platforms: *nix

The Genome Positioning System (GPS) is a software tool to study protein-DNA interaction using ChIP-Seq data. GPS builds a probabilistic mixture model to predict the most likely positions of binding events at single-base resolution. GPS is a Java software, so it runs on multiple platforms,... Platforms: Windows

Ericscript is a computational framework to detect gene fusions from paired end RNA-seq data with high sensitity and specificity. Platforms: Windows, Mac, Linux

SAMMate, a Graphical User Interface (GUI) RNA-seq analysis pipeline, allows biomedical researchers to quickly process SAM/BAM files and is compatible with both single-end and paired-end sequencing technologies. SAMMate automates some of more standard procedures in RNA-seq analysis. Features:... Platforms: Mac

Pyicos is a Deep-seq analysis tool and library written in Python. It???*a*?s designed to be flexible. It can used several in ways: * Command line linux tool * Integrated as part of a bigger pipeline * Auxiliary libraries for python scripting Platforms: *nix

Bio::Restriction::Enzyme is a single restriction endonuclease (cuts DNA at specific locations). SYNOPSIS # set up a single restriction enzyme. This contains lots of # information about the enzyme that is generally parsed from a # rebase file and can then be read back use... Platforms: *nix

Sniffit is a packet sniffer for TCP, UDP and ICMP packets. sniffit is able to give you very detailed technical info on these packets (SEQ, ACK, TTL, Window etc.) but also packet contents in different formats (hex or plain text). Sniffit was actually the start of my TCP/IP experimental phase. As... Platforms: *nix

SYNOPSIS Simplest Each time a new object is created the default style will be slightly different. use PostScript::File; use PostScript::Graph::Style; my $file = new PostScript::File(); my $seq = new PostScript::Graph::Sequence(); while (...) { my $style = new... Platforms: *nix

ETrace is a configurable static port network tracing tool, similar to traceroute, but supporting ICMP, TCP, UDP and other IP protocols. Usage: etrace [ -BbCcnv ] [ -p profile ] [ -F config ] [ -i interface ] [ -I icmp-type ] [ -T port ] [ -U port ] [ -P protocol ] [ -r probe-count ] [ -t... Platforms: *nix

Bio::AnnotationCollectionI is a Perl interface for annotation collections. SYNOPSIS # get an AnnotationCollectionI somehow, eg $ac = $seq->annotation(); foreach $key ( $ac->get_all_annotation_keys() ) { @values = $ac->get_Annotations($key); foreach $value ( @values ) { # value is an... Platforms: *nix

Bio::PrimarySeqI is a Perl Interface definition for a Bio::PrimarySeq. SYNOPSIS # Bio::PrimarySeqI is the interface class for sequences. # If you are a newcomer to bioperl, you should # start with Bio::Seq documentation. This # documentation is mainly for developers using # Bioperl. #... Platforms: *nix

Bio::Index::Swissprot is a Perl Interface for indexing (multiple) Swissprot .dat files (ie flat file swissprot format). SYNOPSIS # Complete code for making an index for several # Swissprot files use Bio::Index::Swissprot; use strict; my $Index_File_Name = shift; my $inx =... Platforms: *nix

IPTables log analizer displays Linux 2.4 iptables logs (rejected, acepted, masqueraded packets...) in a nice HTML page (it support rough netfilter logs but also Shorewall and Suse Firewall logs). This page shall be easy to read and understand to reduce the manual analysis time. This page... Platforms: *nix

Bio::Factory::SeqAnalysisParserFactoryI is a Perl interface describing objects capable of creating SeqAnalysisParserI compliant parsers. SYNOPSIS # initialize an object implementing this interface, e.g. $factory = Bio::Factory::SeqAnalysisParserFactory->new(); # obtain a parser object... Platforms: *nix

Bio::Factory::SequenceFactoryI is a Perl interface that allows for generic building of sequences in factories which create sequences (like SeqIO). SYNOPSIS # do not use this object directly it is an interface # get a Bio::Factory::SequenceFactoryI object like use Bio::Seq::SeqFactory; my... Platforms: *nix

Avast-ng project is A Versatile Ajax Syslog Tailer for syslog-ng. Avast-ng gives you the ability to sift through vast amounts of log files, and display current syslog data which is useful to you. Its a heads up view, that sifts out all the normal flotsam in your log files, and just displays... Platforms: *nix

DB_File is a Perl5 access to Berkeley DB version 1.x. SYNOPSIS use DB_File; [$X =] tie %hash, DB_File, [$filename, $flags, $mode, $DB_HASH] ; [$X =] tie %hash, DB_File, $filename, $flags, $mode, $DB_BTREE ; [$X =] tie @array, DB_File, $filename, $flags, $mode, $DB_RECNO ; $status =... Platforms: *nix

UML::Sequence::JavaSeq is a Perl module for use with genericseq.pl script, works on compiled Java programs. SYNOPSIS genericseq.pl UML::Sequence::JavaSeq Hello.methods Hello > Hello.xml seq2svg.pl Hello.xml > Hello.svg OR genericseq.pl UML::Sequence::JavaSeq Hello.methods Hello |... Platforms: *nix