Search Results for "coordinates"
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Showing 17 open source projects for "coordinates"
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crossmap
convert genome coordinates betweeen assemblies
CrossMap is a program for convenient conversion of genome coordinates and genomeannotation files between assemblies (eg. lift from GRCh36/hg18 to GRCh37/hg19 or vice versa).It support file in BAM, SAM, BED, Wiggle, BigWig, GFF, GTF format. -
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YeastpRofileSpearman
Software to calculate profiles around TSS and TTS of yeast mRNAs
...The input file must be a BedGraph formatted file based on yeast genome sequence release R64. The output file is a text tab-delimited table reporting Rs values for the various shifts of variable coordinates with respect to TSS or TTS. 1) V. Pelechano et al., Nature, 497 (2013) 127-13. -
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YeastpRofile
Software to calculate profiles around TSS and TTS of yeast mRNAs
...The input file must be a BedGraph formatted file based on yeast genome sequence release R64. The output file is a text tab-delimited table reporting R values for the various shifts of variable coordinates with respect to TSS or TTS. R related to each strand is also reported to verify that a similar profile is obtained in the two direction of transcription. 1) V. Pelechano, W. Wei, L.M. Steinmetz, Extensive transcriptional heterogeneity revealed by isoform profiling, Nature, 497 (2013) 127-13. -
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PDBManip
PDBManip is a free program for editing PDB (Protein Data Bank) Files
PDBManip is a free program for editing and manipulating PDB (Protein Data Bank) files. It has a graphical user interface and it is provided as an executable file for running on Windows® operating systems. There is a bunch of free programs on the internet for the same purpose. What discriminate between PDBManip and those programs is that PDBManip uses AngelScript language which is very similar to C/C++ language, to write scripts to do our editing tasks. I know that the text-manipulation... -
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Visualization of Protein-Ligand Graphs
Compute protein graphs. Moved to https://github.com/MolBIFFM/PTGLtools
...The Visualization of Protein-Ligand Graphs (VPLG) software package computes and visualizes protein graphs. It works on the super-secondary structure level and uses the atom coordinates from PDB files and the SSE assignments of the DSSP algorithm. VPLG is command line software. If you do not like typing commands, try our PTGL web server: http://ptgl.uni-frankfurt.de/ -
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MDA
Molecular Dynamics Analyzer (MDA)
...The particle fitting routine is provided by an external library written in C. The results can be exported into the Matlab Workspace or the trackID, frameID and xyz coordinates are saved into files. -
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RT-alignment
Graph-based time alignment algorithms for multiple LC-MS datasets
Liquid chromatography coupled to mass spectrometry (LC-MS) is the dominant technological platform for proteomics. An LC-MS analysis of a complex biological sample can be visualized as a “map” of which the positional coordinates are the mass-to-charge ratio (m/z) and chromatographic retention time (RT) of the chemical species profiled. Label-free quantitative-proteomics requires the alignment and comparison of multiple LC-MS maps to ascertain the reproducibility of experiments or reveal proteome changes under different conditions. The main challenge in this task lies in correcting retention time shifts, which are inevitable even on the same instrument and under the same elution conditions. ... -
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Gen3D
A tool for 3D genome and chromosome structural model construction
Gen3D is an application designed to determine three-dimensional genome and chromosome models. It uses chromosomal contact data to construct three-dimensional conformations. This method can generate three-dimensional chromosomal models satisfying a large portion of chromosomal contacts. The software is developed in Prof. Jianlin Cheng's Bioinformatics, Data Mining and Machine Learning Laboratory in the Computer Science Department at the University of Missouri - Columbia, USA. The project... -
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MSL
http://dx.doi.org/10.1002/jcc.22968
MSL is a C++ library that enables the computational study of macromolecules. The MSL library is not a program (although some applications are distributed) but a tool for scientist to code their own molecular modeling methods. Philosophy The main goal is to create a set of tools that enable the computational study of macromolecules with relative ease at all levels, from simple operations (for example, load a PDB and measure a distance or edit a dihedral) to complex applications... -
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Online Signature Verification
Real time signature verification using MATLAB and C#
...An individual can sign on the digitizing tablet using the special pen regardless of his signature size and position. The signature is characterized as pen-strokes consisting x-y coordinates and pressure with the data being stored in a signature database. Dynamic time warping (DTW) and quadratic discriminant analysis (QDA) is used to get results where the system accepts 2% of forged signatures and rejects 5% of true signatures -
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Darwin_Test 3.3
Darwin Test is a software application to validate and correct records
Darwin Test is a software application to validate and correct records from standards Darwin Core 1.2, Darwin Core 1.4 and Darwin Core Archive. It also can generalize or delete coordinates in those records of the Darwin Core that are considered sensitive data. -
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SeqHunter2
a stand-alone bioinformatics software for querying genome sequences
...It is programmed with the following functions: 1) collect and manage local sequence databases; 2) run blast search by using a batch of sequences and with abundant output formats; 3) extract sequences by a set of IDs or coordinates; 4) generate sequences alignment; 5) edit sequence and translate nucleotide to proteins; 6) browse genome and search genes; 7) collect resource items and link to the website. The full version collects all available oomycete plant pathogens genome sequences and information of research related resource, while the lite version is flexible for non-oomycete users to collected the data they are interested. -
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this script is to visualize the coordinates data. the input is ncbiblast tabular format or a simple coordinates file. output is a png graph file
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Simple python code that produces color-coded quality plots based on fastq format read quality scores. Scores are averaged over binned read tile coordinates. Useful for spotting spatial quality patterns.
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The goal of Picklist Editor is to display and modify pick lists before spot picking (in proteomics).
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OBExtensions is a extension library for the chemoinformatics library Openbabel. It provides extensions to Openbabel, being mostly GUI widgets. OBExtensions has a 2D/3D viewer, 2D coordinates generator and some other extensions.
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This collection of tools written in C++ with the STL library provides the basic building blocks to develop complex analysis pipelines on genomic coordinates.
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