Alignment

JFinisher is software for alignment, editing and manipulation of biological sequences. It aims to assist in the finishing of genome assembly. Starting from a reference sequence, the program align contigs using Smith-Waterman local alignment algoritm with auxiliary methods, allowing management of...

KADMOS provides a lightweight API for alignment of OWL 2 ontologies. It is based on the OWL API v3.

MapPSO is a tool for Ontology Alignment, which uses Discrete Particle Swarm Optimisation. A particle swarm is used to search for the optimal alignment. The algorithm is massively parallel and adapts naturally on parallel architectures.


Platforms: Windows, Mac, Linux

Global optimal sequence alignment using the Needleman-Wunsch algorithm. Aligns DNA, RNA, protein sequence and more! See our sister project local alignment using Smith-Waterman: http://sourceforge.net/projects/smithwaterman/


Platforms: Mac, BSD, Linux

A tool to compare two Protein Sequences and show similarities with the help of dotplot.


Platforms: Windows, Mac, Linux

Sequence studio main package provides classes and interfaces for various kinds of sequence alignment. Differently from regular expressions it computes similarity with two initially unknown strings. Project page provides code generating applet.


Platforms: Windows, Mac, Linux

An implementation of the Smith-Waterman local sequence alignment algorithm. See our sister project global alignment using Needleman-Wunsch: http://sourceforge.net/projects/needlemanwunsch/


Platforms: Mac, BSD, Linux

About Writing Direction Menu Features - Accessible menubar menu - Dynamic indication of the writing direction - Convenient keyboard shortcuts - Set multiple paragraphs writing direction in one action - Smart text alignment based on writing direction - Change the direction of locked text, such as...


Platforms: Mac

BlastViewer provides an interactive graphical user interface for the analysis of the reports produced by the BLAST sequence database search system. BlastViewer is an easy to use software designed for everyday biological sequence analysis relying on BLAST. It allows an easy visualisation and...


Platforms: Mac, Java 1.5 or later

Computes the Woody average by first aligning individual signals (corrupted by jitter) with the standard average. Uses xcorr to compute the lag and then re-averages the signals to get an improved estimate.Example included in help.Technique deteriorates at low SNRs.


Platforms: Matlab

This tool enhances signal detection for broad-mass TOF spectra by accounting for changing peak width and providing peak-shape-dependent filtering capabilities. A set of input TOF spectra is processed to produce aligned peak list and array of corresponding signal intensities. Signal processing...


Platforms: Matlab

NCBI has an implementation of BLAST algorithm on their website at www.ncbi.nlm.nih.gov/BLAST, which is good if you want to query short DNA or protein sequence against various sequence databases. The problem arises when large sequences need to be BLAST'ed against a sequence database or against...


Platforms: Matlab

The icoshift tool for Matlab is an open source and highly efficient program specifically designed for solving signal alignment problems in metabonomic NMR data analysis, but it can also properly deal with other spectra-like datasets (e.g. data from other spectroscopic methods or chromatographic...


Platforms: Matlab

Compared with other Joomla! Adsense modules, JoomSense is definitely the best simple solution for implementing Google AdSense ads on your site! It's much safer and easy to set up. Just input four parameters and it's done! What's more, you can set the ad alignment to left, center or right. Of...


Platforms: PHP

This class is meant to compose and output the contents of an HTML table similarly to the VSFlexGrid component for Visual Basic.It supports defining in a first step the contents and presentation style details of table headers and data rows like colors, alignment, width, etc.. Then in a second step...


Platforms: PHP

SQL2TXT select data of PostgreSQL DataBase by SQL instructions and write results into TXT file (SDF). Alignment and lenghts of columns are configurable.


Platforms: PHP

Twitter has come into almost every blog and so does the twitter related applications. I shared a twitpic API class on my blog recently and after that I have got many requests about a sharing the code which allows you to insert an image from the twitpic.com into the blog posts. However instead of...


Platforms: PHP

Allows you to feature pages on your sidebar using an excerpt of the page and a text or image link to the page. * NEW: Added an option to set what tags are allowed in excerpts. * Set up a random featured page by selecting multiple pages on the widget form. * Added option to hide the widget if only...


Platforms: PHP

This widget will easily allow you to display the "Biographical Info" of any blog author's user profile in the sidebar. It allows you to choose from multiple authors/users on the blog, if your blog does, in fact, have multiple authors. Subscribers are excluded for obvious reasons.Additionally, the...


Platforms: PHP

When you are creating a website for a customer in WordPress sometimes you need not only design a nice theme, but also customize the administration area with customer's colors and logos. Customize your WordPress admin area and login screen with your logos and your color scheme. MyPress also gives...


Platforms: PHP