Jalview A free multiple alignment editor written in Java
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Jalview Tags

view fetch edit alignment editor protein viewer Sequence Fetcher

Jalview Description

A free multiple alignment editor written in Java Jalview is an open source tool used widely in a variety of web pages (e.g. the EBI Clustalw server and the Pfam protein domain database) but is available as a general purpose alignment editor. Here are some key features of "Jalview": User Interface: · Linked highlighting of codon and amino acid from translation and protein products · Linked highlighting of structure associated with residue mapping to codon position · Sequence Fetcher provides example accession numbers and 'clear' button · MemoryMonitor added as an option under Desktop's Tools menu · Extract score function to parse whitespace separated numeric data in description line · Column labels in alignment annotation can be centred. · Tooltip for sequence associated annotation give name of sequence Web Services and URL fetching: · JPred3 web service · Prototype sequence search client (no public services available yet) · Fetch either seed alignment or full alignment from PFAM · URL Links created for matching database cross references as well as sequence ID · URL Links can be created using regular-expressions Sequence Database Connectivity: · Retrieval of cross-referenced sequences from other databases · Generalised database reference retrieval and validation to all fetchable databases · Fetch sequences from DAS sources supporting the sequence command · Import and Export export annotation rows as CSV for spreadsheet import · Jalview projects record alignment dataset associations, EMBL products, and cDNA sequence mappings · Sequence Group colour can be specified in Annotation File · Ad-hoc colouring of group in Annotation File using RGB triplet as name of colourscheme · VAMSAS Client capabilities (Experimental) · treenode binding for VAMSAS tree exchange · local editing and update of sequences in VAMSAS alignments (experimental) · Create new or select existing session to join · load and save of vamsas documents Application command line: · tree parameter to open trees (introduced for passing from applet) · fetchfrom command line argument to specify nicknames of DAS servers to query for alignment features · dasserver command line argument to add new servers that are also automatically queried for features · groovy command line argument executes a given groovy script after all input data has been loaded and parsed Applet-Application data exchange: · Trees passed as applet parameters can be passed to application (when using "View in full application") Applet Parameters: · feature group display control parameter · debug parameter · showbutton parameter Applet API methods: · newView public method · Window (current view) specific get/set public methods · Feature display control methods · get list of currently selected sequences New Jalview distribution features: · InstallAnywhere Installer upgraded to IA 2008 VP1 · RELEASE file gives build properties for the latest Jalview release. · Java 1.1 Applet build made easier and donotobfuscate property controls execution of obfuscator · Build target for generating source distribution · Debug flag for javacc · .jalview_properties file is documented (slightly) in jalview.bin.Cache · Continuous Build Integration for stable and development version of Application, Requirements: · Java

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