Search Results for "script-api.jar" - Page 2
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Showing 44 open source projects for "script-api.jar"
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CRUMp
A probabilistic prediction system of protein phosphorylation sites
...Given an input set of protein sequences in FASTA format, the system outputs the position, residue type (S, T, or Y), and the estimated probability of each tested site being phosphorylatable. Latest downloadable files: - crump-0.2.0.tar.gz: CRUMp GNU Octave package - crump-0.2.0.zip: CRUMp MATLAB script - crumptestset.fasta: A testing dataset in FASTA format. The sequence headers list the accession number of the protein sequence and the position numbers of known phosphorylation sites. Note that CRUMp may predict additional phosphorylation sites that have not been experimentally verified yet. The testing dataset is from Biswas et al. 2010, http://www.biomedcentral.com/1471-2105/11/273/additional. -
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RMol : SD/Molfile information in R
RMol: Transforming SD/Molfile structure information into R Objects
RMol is an R script with a collection of functions to link information of SD/Molfile structure databases with powerful graph analysis packages in R. -
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If you manage phylogenetic data, Bio::NEXUS can make your life easier with a library and ready-made tools to manipulate and visualize NEXUS files (see http://www.molevol.org/nexplorer and http://search.cpan.org/dist/Bio-NEXUS/doc/Tutorial.pod).
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Protein ALignment Optimiser (PALO) is a script for the selection and alignment of the best combination of transcripts among orthologous genes. PALO is mainly written in Python, although other programming languages are also implemented (R, Perl...).
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A batch primer selection program designed to select PCR oligos for gap closure for assemblies containing a large number of gaps. BOSS will select oligos for gap closure of both contig and scaffold gaps. See readme for details.
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t2prhd is a Perl script which generates simple diagrams that highlight relationships of sequence repeats detected by using a profile HMM in two sequences. Homology relations are identified on the basis of the phylogeny of repeats.
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The VRML97-Import-Script is a Python-Script, that extends the capabilities of Blender to import VRML97-Files. It supports Blender since version 2.42.
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BCAR is a library for the associative classification, which denotes "Boosting Class Association Rules". BCAR provides a general tool for classification tasks with various types of input data.
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A perl script that converts Illumina qseq files into Phred fastq files for use in Maq. Originally written by Tyler Bachman from UC Riverside, adapted by Eugene Goltsman. Freely available under the terms of GNU GPLv3.
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dna2abc turns DNA sequences into musical sequences. The key feature is the rule editor; a rule is a regular expression paired with a Tcl script. dna2abc scans a DNA sequence, testing each regular expression: if it matches, the Tcl script is run.
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Phyloview is a perl based CGI script for visualizing taxonomic properties of protein phylogenetic trees.
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Plotamber is a Perl script for an easy and automated plotting of properties derived from molecular dynamics or minimization calculations done with Amber, NAMD or Charmm.
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Amplicon is a Python script for designing PCR primer sets. Amplicon is written in Python 2.3 and Tkinter 8.4. The current script was created for Windows and an executable is available. Future versions of the script should be able to run on Linux and Mac
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For interactive clustering and visualization, Cluster and TreeView by Mike Eisen are great. XCluster by Gavin Sherlock solves the problem of clustering large numbers of files. Now slcview allows you to script generation of cluster and tree images.
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RmscopII is a Tcl/Tk script responsible to redirect protein structure files (PDB files) or RasMol scripts to multiple RasMol sessions. It can be used as a web browser helper application or as a standalone program.
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cel2fr
Tool to convert Affy cel files to be Illumina Final Report compatible
cel2fr is a perl script that can be used to convert Affymetrix CEL files into a format matching an Illumina Final Report. The primary use of this tool is to work in concert with the CNV analysis tool CNVision (www.cnvision.org), but its use is ideal for meta-studies combining multiple datasets. Current version is not yet functional. -
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Python script for Recoord Project (http://www.ebi.ac.uk/msd-srv/docs/NMR/recoord/main.html). It uses Condor and Parallel Python.
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motif_counter
Program to pull out specific motifs from bam sequence files
Motif counter is a simple bash script that allows users to scan all reads contained in a bam file for a specific motif sequence repeated a number of times. Designed to look for the number of variant telomere repeats and reads in a whole genome sequencing dataset. The program prompts for a character string, and the number of times that string should be present in each read, then pulls out the data.
