Sequence Assembly Gap

A fully developed set of DNA sequence assembly (Gap4 and Gap5), editing and analysis tools (Spin) for Unix, Linux, MacOSX and MS Windows.

ABySS-Explorer is an interactive Java application that employs a novel graph-based representation to display a sequence assembly and associated meta data. The tool was designed with the ABySS sequence assembler in mind and was motivated by the need to examine assembly structure, in particular...

LIGR Assembler is a sequence assembly program. It was derived from TIGR Assembler and addresses some of TIGR Assembler's shortcomings.


Platforms: *nix

DIY Genomics is an open source bioinformatics consortium intended to bring a collection of tools and libraries into the hands of small scale genomics labs for the process of sequence assembly and annotation. Projects include DIYA, MGAP, CRISPR, and DIYGV


Platforms: Windows, Mac, Linux

Algorithm::NeedlemanWunsch is a sequence alignment with configurable scoring. SYNOPSIS use Algorithm::NeedlemanWunsch; sub score_sub { if (!@_) { return -2; # gap penalty } return ($_[0] eq $_[1]) ? 1 : -1; } my $matcher = Algorithm::NeedlemanWunsch->new(&score_sub); my $score =...


Platforms: *nix

The whole genome shotgun approach to genome sequencing results in a collection of contigs that must be ordered and oriented to facilitate efficient gap-closure. We present a new tool OSLay that uses synteny between matching sequences in a target assembly and a reference assembly to layout the...


Platforms: Mac

Statistics::Gap Perl module is an adaptation of the Gap Statistic. SYNOPSIS use Statistics::Gap; $predictedk = &gap("prefix", "vec", INPUTMATRIX, "rbr", "h2", 30, 10, rep, 90, 4); OR use Statistics::Gap; $predictedk = &gap("prefix", "vec", INPUTMATRIX, "rbr", "h2", 30, 10, rep, 90, 4,...


Platforms: *nix

UML::Sequence is a Perl module to render UML sequence diagrams, often by running the code. SYNOPSIS use UML::Sequence; my $tree = UML::Sequence->new(@methods, @outline, &parse_method); print $tree->build_xml_sequence(Title); To use this package, or see how to use it, see genericseq.pl...


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

Chart::Sequence is a sequence Perl class. SYNOPSIS use Chart::Sequence; my $s = Chart::Sequence->new( Nodes => [qw( A B C )], Messages => [ [ A => B => "Message 1" ], [ B => A => "Ack 1" ], [ B => C => "Message 2" ], ], ); # or # my $s = Chart::Sequence->new( SeqMLInput =>...


Platforms: *nix

Sequence Analysis project is a collage of coding projects which I have written over the past several years for various clients in my work as a bioinformatics consultant. These clients have graciously allowed me to release these works into the public domain as freeware for Macintosh OS X in...


Platforms: *nix

The FastPCR software was developed to be an integrated tools environment that provides comprehensive facilities for designing primers for most PCR applications including standard, long distance, inverse, real-time, multiplex, unique and group-specific; overlap extension PCR (OE-PCR)...


Platforms: Windows, XP, 2003, Windows Vista, XPX64, 7, 7x64

Short Sequence Location Mapper loads the sequences, then aligns them and finally graphs and tables can be generated for one or more datasets at the same time. SSLM typically works with a BLAST data output file of short Solexa reads mapped to RNA subjects (for example pre-miRNA sequences). The...


Platforms: Windows

Creates an Excel spreadsheet report about the video clips, audio clips and markers you've used in your edited sequence. The report includes sheets for: Clips, Sequence Markers, Clip Markers, Clip Filters, and Reels. Sequence Clip Reporter takes the tedious work out of creating clip usage reports...


Platforms: Mac

Assembly Analyzer allows the user to view the resources and metadata contained within .NET assemblies. It also contains a disassembler that displays source code for methods and dependencies, including call graphs. The latest stable build includes both a ClickOnce installer and a .zip file...


Platforms: Windows

The fastest way to remove duplicates from a sequence depends on some pretty subtle properties of the sequence elements, such as whether they're hashable, and whether they support full comparisons. This script defines the unique() function that tries three methods, from fastest to slowest,...


Platforms: Windows, Mac, *nix, Python, BSD Solaris

This script contains a function that given a sequence and a number n as parameters, returns the th permutation of the sequence (always as a list).


Platforms: Windows, Mac, *nix, Python, BSD Solaris

This script allows you to split up a sequence in same-size (if possible) parts.


Platforms: Windows, Mac, *nix, Python, BSD Solaris

Getting min/max in a sequence script allows you to find the min/max value in a sequence as compared to a reference.


Platforms: Windows, Mac, *nix, Python, BSD Solaris

This function provides farey sequence, F(n), for any integer n.There's probably a more elegant solution out there, but I couldn't find it. Note: it doesn't prepend (0,1) and append (1,1)...


Platforms: Windows, Mac, *nix, Python, BSD Solaris