Search Results for "convert"
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Showing 33 open source projects for "convert"
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MView
Extract and reformat a sequence database search or multiple alignment
.... ---- MView is a command line utility that extracts and reformats the results of a sequence database search or a multiple alignment, optionally adding HTML markup for web page layout. It can also be used as a filter to extract and convert searches or alignments to common formats. Inputs: - Sequence database search: BLAST, FASTA suites. - Multiple sequence alignment: CLUSTAL, HSSP, MSF, FASTA, PIR, MAF. Outputs: - HTML, FASTA, CLUSTAL, MSF, PIR, RDB (tab-separated). Found a bug? Please open an issue on the MView issue tracker at https://github.com/desmid/mview/issues or send an email to biomview@gmail.com. -
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CpDB
Relational database schema and tools for bacterial genome annotation
This software allows us to create a relational database in PostgreSQL hosting full bacterial genomes. Besides the database, there is software, like a parser, to convert EMBL or GBK files to the CpDB relational schema. Once in the CpDB, one can extract unlimited reports from bacterial genomes using SQL. This software is part of the Ph.D. in Bioinformatics from Anderson Santos (https://orcid.org/0000-0003-3418-0823) developed under the Corynebacterium pseudotuberculosis (Cp) pangenome project. The Cp pangenome delivered to the scientific community fifteen bacterial strains deposited at the GenBank database between the years of 2009 and 2012. ... -
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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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...The SBFC Web Site providing detailed feature description and instructions for installing, using and developing new modules is: http://sbfc.sourceforge.net/ . Currently, SBFC allows the user to convert SBML models into the formats: BioPax, Matlab, Octave, XPP, DOT, and SBGN. Due to its modular design fast development and addition of new converters is highly facilitated. SBFC can be executed in two modes: 1. standalone executable downloading the package provided in this website; 2. web-service at http://www.ebi.ac.uk/biomodels/tools/converters . ...
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Enterprise-grade ITSM, for every businessFreshservice is an intuitive, AI-powered platform that helps IT, operations, and business teams deliver exceptional service without the usual complexity. Automate repetitive tasks, resolve issues faster, and provide seamless support across the organization. From managing incidents and assets to driving smarter decisions, Freshservice makes it easy to stay efficient and scale with confidence.
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MSP Builder 2
Converts text files (such as csv, tsv, txt) to MSP files
Take a list from a search and how do you use that as a search. Answer: As an MSP file. But how do you make one? Answer: With this app. Convert your csv etc files to MSP. You define the relationship (the mapping) and take it from there. Includes a couple of examples. -
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MSP2MGF
Convert MSP files to MGF files - Only you know why
MSP2MGF processes MSP data files (NIST standard text files for searching) It: converts MSP data files into MGF files (mascot generic format)., produces a new file with the same name as your input file's, allows you to change the mapping of MGF fields into MGF fields, has a command line interface so you can pass files in programatically. You: either drag and drop MSP files onto the window, or pass filenames though a command line argument. Command line... -
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CusVarDB
CusVarDB generated variant protein database from NGS-datasets
...Annotate the variant using ANNOVAR 4. Create the variant protein database Apart from the main modules, the program also supports additional functions such as 1. Download the SRA 2. Convert the SRA file to fastq file format 3. Download the annotation (ANNOVAR) database and Dry-run concept to customize the commands Executables are available at http://bioinfo-tools.com/Downloads/CusVarDB/V1.0.0/ Test dataset is available at http://bioinfo-tools.com/Downloads/CusVarDB/V1.0.0/test_dataset.rar -
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MGF2MGF CH
Convert mgf mass values to their nearest elemental formula
MGF2MGF CH processes mgf files (mascot generic format). It: converts masses to their nearest elemental formula mass (provided that you supply an empirical formula), can normalise intensities to the base peak of a block of ions, produces a new file with the prefix of your choice. You: specify the input line that contains the empirical formula of the parent ion, specify the key that identifies a formula and then the formula) separated by one space character, either ... -
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MGF 2 FOR-JSON
Conversion of MGF files to JSON format
Want to convert an MGF file to JSON format? This is the app for you, especially if you want to use the JSON file in the FOR-IDENT search program. If you don't know what MGF file, JSON format, FOR-IDENT search program is then this isn't the app for you. Happy conversion! -
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Peptide3D 2 MGF
Converter for Peptide3D.xml to MGF
Ever wanted to make an MGF file from a Peptide3D.xml output? If so then this is for you. Simply drag the xml onto the window and that's it. All the information needed is contained within the xml file. You get your mgf in the same place, same name, different extension. -
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...The software has been optimized for microarray and deep parallel sequencing data, however it can accept any character delimited tabular data sets. HTDP can also import, process and convert Variant Call Format (VCF) files ver. 4.0, 4.1 and 4.2 (http://samtools.github.io/hts-specs/VCFv4.2.pdf). HTDP provides quick filtering functionality and can process data consisting of single or multiple input files. Citation: Madanecki P, Bałut M, Buckley PG, Ochocka JR, Bartoszewski R, Crossman DK, et al. (2018) High-Throughput Tabular Data Processor – Platform independent graphical tool for processing large data sets. ...
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fcGENE: Genotype format converter
Format converting tool for genotype Data (e.g.PLINK-MACH,MACH-PLINK)
...Further application: -obtaining templates of necessary imputation commands and commands of other imputation tool - Quality control according as MAF,HWE & CALLRATE. key words: genotype transformation, convert genotype format, imputation output, PLINK, IMPUTE, MACH, minimac, HAPLOVIEW, BEAGLE, BIMBAM,EIGENSOFT. -
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Java bio-informatics library to analyze and convert genomic sequence and assembly data. This library was created and used by the J. Craig Venter Institute (JCVI)
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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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KAnalyze
DNA/RNA Sequence K-mer Toolkit
KAnalyze is a Java toolkit designed to convert DNA and RNA sequences into k-mers. It is both a command line application and an API. -
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The Systems Biology Results Markup Language is a language describing data. Unlike flat data formats, SBRML allows describing the origin of the data as well. This project hosts a library and tools for using SBRML.
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ConvertMAS
ConvertMAS converts Chemical File Formats mol, mol2 and sdf.
ConvertMAS - molecule converter; use to convert Chemical File Formats. It works on mol, mol2 and sdf files. It converts single file to respective formats. It will split sdf file with multiple molecules into seperate single files of any desired format. Also ConvertMAS creates sdf files from joining of mol, mol2 and sdf files. This is stand alone application; hence no need of internet connectivity to get results. -
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FASTQSim
NGS data characterization and in silico read generation
...FASTQSim is sequencing platform-independent, and computes distributions of read length, quality scores, indel rates, single point mutation rates, indel size, and similar statistics for any sequencing platform. To create training or testing datasets, FASTQSim has the ability to convert target sequences into in silico reads with matching error profiles. FASTQsim allows the user to simulate individual read datasets that can be used as standardized test scenarios for planning sequencing projects or for benchmarking metagenomic software. In this regard, in silico datasets generated with the FASTQsim tool hold several advantages over natural datasets: they are sequencing platform independent, extremely well characterized, and less expensive to generate. -
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This script can convert raw diffraction images to JPEG files. Support ADSC, MarCCD, Mar345, RAXIS and PILATUS, and can be run on Windows, Linux and Mac OS X.
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Athus
Manage, merge, filter and convert population genetics data
This project assists you in performing population genetic analyses by taking over the ugly, boring and error-prone data manipulation steps. Starting from well specified input formats VCF, BED and FASTA and a unique configuration file describing data (f.e. from SNP-arrays or sequencing) as well as filtering one can create standard POPGEN formats like Eigenstrat, PEDMAP (PLINK), Treemix ... In addition there are several utilities for * generating VCF from SNPArray data (NCBI - GEO,... -
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Genetic data converter
Convert genetic data for hapmixmap software
Genetic data converter, for hapmap.org and hapmixmap data formats. Reads data in tabular format and writes in hapmixmap format. It's possible to add extensions to output different data formats. -
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Utility to convert PED genome file into RAW SNP format. Creates multiple files per person. Supports big files. The same conversion utility has been included into "aisconvert" toolkit, so this project is rather deprecated.
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H-mito is a mitochondrial DNA haplogroup prediction tool based on the phylogenetic tree http://www.phylotree.org/. Ancillary scripts: mitoP.py to extract mutation lists and clustal-2-fasta.zip to join, align through clustalw and convert data.
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The DNA Sequence Read Toolkit is a set of programs to convert data from DNA sequencing instruments into formats suitable for archiving, viewing or for onward processing (for example alignment or assembly).
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These scripts written in Python allow you to convert fasta files into multifasta file and vice versa.
