Search Results for "motif file"
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Showing 18 open source projects for "motif file"
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1
XFile - File Manager
File manager for Unix (X11/Motif)
XFile is a compact file manager for Unix and alike systems running X11. It presents the file system as is, without imaginary locations, trashcans etc. XFile uses its own file type/association database in typical Unix/RC like syntax, which is easily editable. Mounting support for file systems defined in fstab, and integration with mount daemons that manage a dedicated media directory is also included. XFile is easily configurable and customizable with X resources, and has no dependencies, save... -
2
rename tool extension
A portable file rename tool
A file rename tool can rename, lowcase, upcase large numbers of files. It's a quick and powerful tool written in C with extended regular expression supporting for searching and substituting pattern strings in filenames. Support Linux and Windows. -
3
XImaging
Image browser and viewer for Unix - X/Motif
XImaging is a lightweight, multi-threaded image browser and viewer for Unix - X/Motif, with basic file management functionality. Documentation and more on the project homepage: http://fastestcode.org/ximaging.html -
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Finding DNA Repeats by RFRE
RFRE is a tool to find DNA repeats (tandem and short)
... Regular Expression Tool Regular Expression for Protein Motif Search and SSR sequence. https://sourceforge.net/projects/rfret/files/RFRE122019.exe/download https://www.preprints.org/manuscript/201910.0249/v1 https://sites.google.com/must.edu.eg/finding-dna-repeats/home ---------------------------------------------- *****Very important program must be downloaded before you run the EXE FILE OF RFRE***** 1-VB6 Runtime Plus 2.2.exe , https://sourceforge.net/projects/vb6extendedruntime/ -
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5
Extended Motif FileSelectionBox
Motif file selection box with modern usability features
Standard Motif file selection box is stuck in 1990. Moving to directory up with ".." is incomprehensible to modern users. They expect arrow up. File selection box should offer detail view, not just list view. Detail view should display file size and date, and allow sorting by desired column. Directory path and filter should have drop down menu for recent or typical paths/searches. File selection box should permit creation of a new directory, as well as renaming/deleting existing files... -
6
bxfm
Little file manager for Motif
Little file manager for Motif -
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CRISPR-offinder-v1-2
A CRISPR tool for user-defined protospacer adjacent motif
CRISPR/Cas system undoubtedly holds great potential for genome editing. Target site cleavage by CRISPR technology requires a protospacer adjacent motif (PAM) immediately downstream or upstream of the protospacer element to which the sgRNA binds. However, Cas9 from different types of bacteria or variant recognizes different PAM sequences. To meet the needs of different CRISPR system with specific and efficient sgRNA design, CRISPR-offinder was developed. Given an input FASTA file of the target... -
8
mkmap
A map maker via online map services
Mkmap is a map maker by downloading map tiles from online map services, like google maps, and combining into a single large picture file. It accepts the latitude and longitude coordinates, then downloads and merges map tiles. The idea of mkmap is to generate a larger map than the size of a browser screen. So the map could be easily printed or viewed in an off-line device. Mkmap supports Linux and Windows platform. -
9
ISVASE
identification of sequence variant associated with splicing event
To generate correct mature mRNAs, the exons must be identified and joined together precisely and efficiently by RNA splicing mechanism. It is to be noted that about one third or a half of all disease-causing mutations effect RNA splicing. However, there is little bioinformatics tools to directly identify sequence variants associated with splicing events (SVASE) based on RNA-seq data. We developed ISVASE, a simple and convenient tool for identifying SVASE directly using RNA-seq data.... -
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10
XASTIR
Multiplatform Ham Radio APRS and Mapping Program
NOTE: Code commits are FROZEN on SourceForge: New code is now at <http://github.com/Xastir/Xastir>. Real-time tracking & messaging of stations via radio/internet APRS data streams, w/125 map formats supported. Linux/FreeBSD/Solaris/MacOSX/Windows in any of 7 languages. Can also be used for mobile mapping w/GPS. MAILING LISTS ARE AT: PROJECT->WEB SITE. -
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Motif based graphical Hex-dump of files. Includes searching for masked pattern, jump to file position and editing the file-contents. Display is "as is", without any endianess conversion. The file is displayed with address, Hex and text.
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12
PROMOT
A tool for finding functional motifs from aligned protein sequences
PROMOT (version 4.0) is a bioinformatics tool for discovering motifs (in the PROSITE format) from a set of aligned sequences. To run the tool, you need to have Java 8 installed on your system. Download and execute the JAR without any parameters to know about how to use the tool. A sample alignment of 91 protein sequences is also provided in the file "aligned.fasta". A sample run of the tool can be seen by using the following command: java -jar promot4.jar 70 2 n aligned.fasta > output.txt... -
13
NSCR
Nascent Strand Capture and Release Protocol, bioinformatics part
This project is the bioinformatics part of the NSCR protocol paper, including mapping reads to reference sequence, wiggle file generation, motif searching, stiffness and bendability analysis. -
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PANDA
Passing Attributes between Networks for Data Assimilation
PANDA (Passing Attributes between Networks for Data Assimilation), is a message-passing model to gene regulatory network reconstruction. PANDA integrates multiple sources of biological data, including protein-protein interaction, gene expression, and sequence motif information, in order to reconstruct genome-wide, condition-specific regulatory networks. PANDA is also available in other programming languages, including: MATLAB/Octave: (1) https://drive.google.com/a/channing.harvard.edu... -
15
DHC-MEGE
DNase Hypersensitivity Connectivity Motif Enrichment in GeneExpression
... a list of up genes, down genes, a DNase hypersensitivity connectivity map (BED8 format) and genome sequence (fasta format). What is the output? The main output is the GMT file, which is a list of gene lists which details the occurance of sequence motifs across the hypersensitive regions of the genome. How can I use the output file? GMT files can be used in gene set enrichment analysis of the array/mRNA-seq experiment. More info in the manual. -
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wxDC is a cross-platform DC (Direct Connect) filesharing client similar to DC++ written in C++ which runs on Windows (all), Unix/Linux (GTK+, Motif, X11), and MacOS X. wxDC uses the wxWidgets cross-platform SDK which can be found at www.wxWidgets.org.
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Maximal Clique Motif Reduction (MCMR) is a software program for running and then combining the output of multiple motif finder programs, such as MEME, AlignACE and Weeder, into a set of consensus predictions with associated confidence rankings.
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18
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. Motifs can either be consecutive or uncoupled from each other across the read, and analysis...
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