:: DESCRIPTION
blast2malign is an easy to use script that creates a multiple alignment (relative to the query) from the database hits of a BLAST search. Multiple HSPs from a database sequence are combined or separated depending on their relationship to each other.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
SnapGene Viewer is revolutionary software that allows molecular biologists to create, browse, and share richly annotated DNA sequence files up to 1 Gb in length.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
Genes2WordCloud is a word-cloud generator and a word-cloud viewer that is based on WordCram implemented using Java, Processing, AJAX, mySQL, and PHP. Text is fetched from several sources and then processed to extract the most relevant terms with their computed weights based on word frequencies.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Source Code Biol Med. 2011 Oct 13;6:15. doi: 10.1186/1751-0473-6-15.
Genes2WordCloud: a quick way to identify biological themes from gene lists and free text.
Baroukh C, Jenkins SL, Dannenfelser R, Ma’ayan A.
:: DESCRIPTION
CytoscapeRPC is a Cytoscape plug-in which allows users to create, query and modify Cytoscape networks. This means that you can automate your Cytoscape tasks from any programming language which supports XML-RPC
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2011 Sep 1;27(17):2451-2. Epub 2011 Jun 27.
CytoscapeRPC: a plugin to create, modify and query Cytoscape networks from scripting languages.
Bot JJ, Reinders MJ.
:: DESCRIPTION
CREATE is software for the creation of new and conversion of existing data input files for 64 genetic data analysis software programs. Programs are grouped into areas of sibship reconstruction, parentage assignment, effective population size, quantitative genetics, general genetic data analysis, and specialized genetic applications.
::DEVELOPER
Jason Coombs ,jcoombs@cns.umass.edu ,Ben Letcher, and Keith Nislow
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
create: a software to create input files from diploid genotypic data for 52 genetic software programs.
Coombs JA, Letcher BH, Nislow KH.
Mol Ecol Resour. 2008 May;8(3):578-80. doi: 10.1111/j.1471-8286.2007.02036.x.
:: DESCRIPTION
PlasmidForm is a simple Python program to allow BGME students to create plasmid forms fast and simple. This program allows the user to input the sequence in the Fasta format (as from GeneWiz) and automatically generate the plasmid form. The program will take care of translating the sequence into protein and aligning it to the background protein sequence.
::DEVELOPER
Victor Khangulov vkhangulov@jhu.edu @ BGME lab
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
AMINONET is a Java-based software tool to construct different protein contact networks (unweighted and weighted; long range, short range and any range; hydrophobic, hydrophilic, charged or all-amino-acid networks). The networks thus constructed can be visualized. The software will also help in the calculation of the values of the different topological parameters of the constructed networks.
::DEVELOPER
Md. Aftabuddin, Sudip Kundu
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Md. Aftabuddin and S. Kundu
AMINONET – a tool to construct and visualize amino acid networks, and to calculate topological parameters
J. Appl. Cryst. (2010). 43, 367-369
:: DESCRIPTION
ACIB PGDB Toolbox is a plug-in for Pathway Tools, an integrated systems biology software to create, maintain and query Pathway/Genome Databases. Fully integrated into the graphical user interface (GUI) and menu of Pathway Tools, this plug-in provides functions to create multiple sequence alignments, systematically annotate insertion sequence (IS) elements and analyze their activity by cross-species comparison tools. Microarray probes can be automatically mapped to target genes, and expression data obtained with these arrays can be transformed into input formats needed to visualize them in the various -omics viewers of Pathway Tools
::DEVELOPER
Genomics & Bioinformatics Graz, Graz University of Technology
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Krempl PM, Mairhofer J, Striedner G, Thallinger GG.
A Sequence Comparison and Gene Expression Data Integration Add-on for the Pathway Tools Software.
Bioinformatics. 2012 Sep 1;28(17):2283-4.
:: DESCRIPTION
SlideMap.pm is a Perl module used to create a row/column to plate/well map of a microarray slide. It does not as yet incorporate annotation data into the map, but simply creates the map object based on input parameters. The map is an ordered list of spots containing array_row, array_col, plate_alias, well. SlideMap currently supports 5 types of arrayers: IAS, MD, MD3, Lucidia, and Stanford. However, ‘generic’ arrayers can be used with this perl module. SlideMap provides methods for conversion of spots to wells and wells to spots.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
