Analyze 16s Rrna Gene Sequence

OrientationChecker is a simple, Java based application specially designed to help you check and alter the orientation of 16S rRNA gene sequences. Platforms: Windows

Mallard is a handy, Java based application based on the Pintail algorithm designed to work by comparing evolutionary distances between a query and subject sequence over the length of the 16S rRNA gene (small subunit rRNA), by employing a sampling window of specified size, progressing a fixed... Platforms: Windows

A research fellow at Harvard asked me to write a program to search for gene sequence, such as d-de?TCCd-deOao, and record the next 4 codes. The data file was 14Gb. He tried some matlab codes, and the system froze, or kept running and never stopped.I first tested using a loop method (V1.0). It... Platforms: Matlab

Pintail is a tool for identifying anomalies, including chimeras, within 16S rDNA sequences. The program works by comparing evolutionary distances between a query and subject sequence over the length of the 16S rRNA gene (small subunit rRNA), by employing a sampling window of specified size,... Platforms: Mac

The Ribosomal Database Project's Pyrosequencing Pipeline aims to simplify the processing of large 16S rRNA sequence libraries obtained through pyrosequencing. This site processes and converts the data to formats suitable for common ecological and statistical packages such as SPADE, EstimateS, and R. Platforms: Mac

Wormbase Converter is a simple, easy to use application designed to help you with the conversion of any Gene ID into any other Gene ID. You can convert a "WormBase ID", a "Gene/Transcript/CDS Sequence Name" or a "Gene Name" into a "WormBase ID", a "Gene Sequence Name" or a "Gene Name". Moreover,... Platforms: Windows

T-RFPred, Terminal-Restriction Fragment Prediction Tool, is a group of Perl scripts that will help researchers to identify the profile peaks of a T-RFLP fingerprint using clone libraries of partially sequenced 16S rRNA genes from the same sample. Platforms: Windows, Mac, Linux

PhyloTrac is an application for the visualization and analysis of PhyloChip microarrays. The PhyloChip is a popular 16S rRNA gene microarray for microbial surveys, and has been successfully used to study the microbial diversity of several interesting environments. However, its adoption has been... Platforms: Mac

MacVector... Researchers who want a simple but comprehensive desktop sequence analysis application continually turn to MacVector, the leading sequence analysis package for the Macintosh. MacVector provides sequence editing, primer design, Internet database searches, protein analysis, sequence... Platforms: Mac

WinBlast is a handy, easy to use application specially designed to offer you a graphical front-end for NCBI BLAST. Platforms: Windows

IRobot is the Internet-robot engine for Visual Web automation and Web scraping. Completely automatic Web recording. Create your own IRobot Web robot agents to automate everything on the Web. Support Web data integration and computation. Share your Web experience with your friends. Batch form... Platforms: Windows

Gene Inspector is a unique combination of a versatile electronic laboratory research notebook and a comprehensive sequence analysis product. Using GI, the user has the ability to define an entire 'suite of analyses' that can be performed each time they (or anyone in the lab) has a new sequence,... Platforms: Mac

Main Workbench includes all features from CLC DNA Workbench, CLC RNA Workbench, and CLC Protein Workbench, as well as a range of Gene Expression Analysis. CLC Main Workbench creates a software environment enabling users to make a large number of advanced protein sequence analyses, combined with... Platforms: Windows, XP, Windows Vista, XPX64, 7, 7x64

Sequence diagrams are a very effective way of modeling an object oriented system. Unfortunately, most UML based modeling tools only offer primitive support for sequence diagrams. EventStudio provides advanced constructs for sequence diagram based object modeling. EventStudio supports generation... Platforms: Windows

Windows modeling tool that simplifies and speeds up the creation and maintenance of UML sequence diagrams, telecom/wireless call flow diagrams and process workflow diagrams. Sequence Diagram Editor performs automatic layout/formatting (across multiple pages if necessary) and supports additional... Platforms: Windows

GENE Graph Export Engine is an advanced XML exporter. GENE Graph Export Engine is a complex convertor/framework for multi-namespace XML transforming and exporting. It is able to convert various XML types including SVG, DocBook, MathML, XSL-FO, and their combinations into a wide area of output... 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

http-analyze is a log analyzer for web servers. It analyzes the logfile of a web server and creates a comprehensive summary report from the information found there. http-analyze has been optimized to process large logfiles as fast as possible. http-analyze can be used with any web server... Platforms: *nix