PAT 0.9

PAT  is a Java-application for constructing multiple protein sequence alignments from regions of high similarity. It provides tools to identify, mark and align such regions. The sequences and the alignment can be visualized differently, e.g. using a special coloring of the amino acid symbols or displaying the sequences either as strings or schematically as rectangles. As the program is designed as a framework, it can be extended very easily. For example, you can implement and use additional algorithms for analyzing the sequences.

PAT is based on the program MACAW (Schuler GD, Altschul SF, Lipman DJ, 1991) and the implemented algorithm for searching local similarities, of which blocks can be constructed. In this way also protein sequences which share only a few domains can be compared. Global alignment algorithms would not be appropriate here.

The first version of this program was written by Ilka Hoof, Chrstian Klug and Georg Zeller as a student project under supervision of Daniel Huson and Andrei Lupas, Daniel Huson has since worked extensively on the code.

Screenshots

The sequences are displayed in different Views, of which any number can be opened. Currently two types are available: In the Alignment View the sequences are shown as strings, in the Schematic View schematically as recangles.

Using the mouse cursor any sequences or parts of them can be selected and then analyzed by one of the Explorer algorithms, e.g. by the MACAW algorithm, which identifies regions of high similarity.

A block is a set of subsequences of equal length. The Explorer algorithms yield as result a list of blocks, which can then be edited. Those which are deemed to be important can be marked, i.e. saved, and highlighted in the alignment. Marked blocks can be aligned (linked), which happens automatically by inserting gaps ('-') into the alignment.

By the block editor any Explorer result or existing block can be viewed and modified. The quality of a block can be assessed by means of scores and a significance value.

·中生网广告不少，不过都很老实，如果你乐意，请支持本站一下，如果打扰到了你敬请绕过。

·本站提供的软件包含破解补丁及注册码均是由网上搜集，若无意中冒犯了你权利，请联系21doll@163.com，本站立即改正！

·任何涉及商业盈利目的均不得使用，否则产生的一切后果将由你自己承担。