Search Results for "fasta" - Page 2
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Showing 102 open source projects for "fasta"
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mfsizes
Multi-FASTA sequence (DNA or protein) statistics calculator.
A simple command-line utility to calculate biological sequence (DNA or protein) sizes in a (multi) FASTA file. It gives averages, GC (or methionine) content, N50, N90, N95, number of N's, and total bases, and can also report by codon if requested. -
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Genome Downloader
Downloads genome data from NCBI based on search terms.
GenomeDownloader is a command-line Perl program to download genomic data (using wget) from NCBI. It has been recently (2017-10) completely rewritten to work with the "new" data organization structure at NCBI. Assembly completion level (i.e., Contig, Scaffold, Chromosome or Complete Genome) can also be selected as a criterion for downloading data. Genomic data can be downloaded from all organisms belonging to a certain taxon (e.g., Mammalia or 40674), and downloads can be limited to... -
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Genome Profiler
a wgMLST analysis tool for bacterial WGS data
...Please download the latest version from: https://github.com/jizhang-nz Update 4th Oct. 2017: version: 2.1 bugs fixed. Update 8th Sep 2015: When using a multi-Fasta file of the the allele sequences (nt) as reference (switch -n), please use only CAPITAL letters A, T, G and C for the sequences. This bug will be fixed in the next version. -
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CRISPR-offinder-v1-2
A CRISPR tool for user-defined protospacer adjacent motif
...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 sites and queries the reference genome as well as a CRISPR system with a defined spacer length and PAM sequence, this standalone tool will identify putative sites and assign a predicted activity based on support vector machine model which conducted by sgRNA Scorer 2.0. In addition, sgRNAs with minimal off-target activity were predicted by Cas-OFFinder, and score with Off-Target Cutting Frequency Determination (CFD). -
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...It's simple linux program which evaultes the genome assembly with high speed and accuracy. Please read instuctions.md [Options] Argument 1 -> Name of the input fasta/fastaq file Argument 2 -> Sequence Limit (optional)(Default: 999999999) Argument 3 -> Usable scaffold length (optional)(Default: 2500) Argument 4 -> Number of Nucliotide to spit into contigs (optional)(Default: 25) Argument 5 -> Genome size (optional)
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BioFace is simple software for editing and analyzing DNA, RNA, and protein sequences that is written in Java using SWT and JFace as libraries. Opening GenBank, FASTA, EMBL, or simple sequence files and analizing these sequences can be done.
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BioUtils Perl Library
A collection of Perl modules for handling fasta/q sequences and files.
WARNING: BioUtils has been migrated to Github (Nov 2017). For the most up-to-date versions and info please visit: https://github.com/islandhopper81/BioUtils BioUtils are a collection of Perl modules for DNA sequence analysis in bioinformatics. BioUtils is a significantly faster and more memory efficient alternative to BioPerl. However, it's functionality is currently limited to the features listed below. -
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MSTgold
Estimate minimum spanning trees with statistical bootstrap support
...The MSTgold package includes Mac OS X, Linux, and Windows executables of the MSTgold program, a detailed Manual, example data and results, and executables of the program Fasta2MSTG which converts Fasta sequence files to the MSTgold input format. -
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PBSuite
Software for Long-Read Sequencing Data from PacBio
.... ----- PBJelly ----- Read The Paper http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0047768 PBJelly is a highly automated pipeline that aligns long sequencing reads (such as PacBio RS reads or long 454 reads in fasta format) to high-confidence draft assembles. PBJelly fills or reduces as many captured gaps as possible to produce upgraded draft genomes. ----- PBHoney ----- Read The Paper http://www.biomedcentral.com/1471-2105/15/180/abstract PBHoney is an implementation of two variant-identification approaches designed to exploit the high mappability of long reads (i.e., greater than 10,000 bp). ... -
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Kinannote
Protein Kinase Identification and Classification
Kinannote identifies and classifies protein kinases in a user-provided fasta file using an HMM derived from serine/threonine protein kinases, a position specific scoring matrix derived from the HMM, and comparison with a local version of the curated kinase database from kinase.com. If the user inputs a complete proteome, additional modules evaluate the completeness of the kinome and place it in context with reference kinomes. -
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PrAS
predict protein amidation sites
This predictor is developed to predict amidation sites based on support vector machine (SVM) classifier. It is supplied in source code form along with the required data files and run under the linux. The input is a protein sequence file (fasta format) by Tong Wang and Wei Zheng (tongwang.scu@gmail.com and jlspzw139@sina.com) Notice:You should download all zip file in this project! -
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GenomeDatabase
For creating a local database of reference genomes
Genome Database - A tool to create a local database of reference genome sequences Usage: java path/to/GenomeDatabase.jar [options] By Marc Strous, 2016 This tool enables you to download fasta files of protein and RNA sequences encoded in reference genomes at NCBI. You can select relevant genomes with a set of queries. Each query has four fields, separated by comma's. Example of a queries are: superkingdom,Bacteria,genus,ftp superkingdom,Archaea,genus,ftp superkingdom,Eukaryota,phylum,ftp superkingdom,Viruses,family,elink The first query would download (with ftp) all available reference genomes of the superkingdom Bacteria, limited to one genome per genus. ... -
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metawatt
Binner for assembled metagenomes
The Metawatt binner is a graphical binning tool that makes use of multivariate statistics of tetranucleotide frequencies and differential coverage based binning. It also performs taxonomic assessment of binning quality (via diamond BLASTx). Created bins can be edited and exported as fasta. The Metawatt is implemented in Java SWING and minimally depends on Diamond, HMMer3.1, BBMap, Prodigal and the Batik library for the export of SVG graphics. Citation: Strous M, Kraft B, Bisdorf R, TegetMeyer H (2012) The binning of metagenomic contigs for microbial physiology of mixed cultures. Frontiers in Microbial Physiology and Metabolism 3:410. doi: 10.3389/fmicb.2012.00410 -
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converts a SAM file to fasta file. SAM file is a file output from bwa alignment software. It outputs aligned fasta file.
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KA-predictor
lysine acetylation site prediction
This predictor is developed to predict species-specific lysine acetylation sites based on support vector machine (SVM) classifier. It is supplied in source code form along with th e required data files and run under the linux. The input is a protein sequence file (fasta format). -
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RGAAT
Reference based genome assembly and annotation for new genome
This program can assemble and/or annotate genome for new genome and known genome upgrade using sequence alignment file (SAM or BAM format), sequence variant file (VCF format or five coloum table (tab-delimited, including chromosome, position, id, reference allele and alternative allele)) or new genome sequence file (FASTA format) based on reference genome sequence file (FASTA format) and annotation file (TBL, GTF, GFF, GFF3 or BED format). -
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gDNA-Prot
DNA-binding protein prediction software
This program will predict the DNA-binding proteins when input a protein sequence (Fasta format), it is supplied in source code form along with the required data files and run under the windows. -
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Mauve computes and interactively visualizes genome sequence comparisons. Using FastA or GenBank sequence data, Mauve constructs multiple genome alignments that identify large-scale rearrangement, gene gain, gene loss, indels, and nucleotide substutit
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JFASTA
Java implementation for the FASTA file format.
JFASTA is a lightweight framework for handling FASTA files. It supports reading, writing and parsing of single- or multi-FASTA files. Files may be read/ written at once, or stream-based (memory efficient). It's stable, very intuitive and good integrated with Java 1.5 SDK and later. -
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CATO Clone Alignment Tool
Identifies clone sequences corresponding to set of reference sequences
Specialized sequence alignment software that helps associate the most likely matches of clone sequences to a set of reference sequences. Both sets of sequences are assumed to be nucleotides. -
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Protospacer Workbench
CRISPR/Cas9 guide-RNA design
Protospacer Workbench helps to design, analyze, and share CRISPR target-sites for any organism or set of FASTA formatted sequences. Design of guide-RNAs for the CRISPR/Cas genome editing system is intuitively easy, but computationally difficult. The main difficulty arises from the need to identify potential off-targets that may be quite different from the intended target. Current online tools for guide-RNA design provide a user friendly interface to sequence mapping software such as Bowtie or BLAST. ... -
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PanCGP
PanCGP: Pangenome and Comparative Genome Analysis Pipeline tool
...Those results are interpreted in the form of pan-genome, core genome/proteins, dispensable genes/proteins, unique/strain-specific genes/proteins, new gene/protein families and total number of genes per strain of the specie. It also extracts the corresponding protein sequences against pan-genome, core protein and dispensable protein sequences in separate FASTA formatted text files. The tabular text format can be used to render the final results in the form of visual graphs representing the trends in gene/protein sequence analysis. -
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ArtificialFastqGenerator
Ouputs artificial FASTQ files derived from a reference genome.
ArtificialFastqGenerator takes the reference genome (in FASTA format) as input and outputs artificial FASTQ files in the Sanger format. It can accept Phred base quality scores from existing FASTQ files, and use them to simulate sequencing errors. Since the artificial FASTQs are derived from the reference genome, the reference genome provides a gold-standard for calling variants (Single Nucleotide Polymorphisms (SNPs) and insertions and deletions (indels)). -
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Software for visualization of point variability in pairwise sequence alignment FASTA format. Featuring GUI interface, this simple application enables insight into variation of nucleic and amino acids on specific loci. Current 1.1 version supports amino and nucleic acid alignments. There are 2 variations of this software. One is CLI based and the other one is GUI based. Read corresponding README files in order to get familiar with the software.
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iMSAT represents a full update of the vcf2MSAT program. This command line python program allows for a user to use the polymorphism data generated using SAM- and BAM-tools and a .fasta alignment file to search for polymorphic microsatellite markers (MSATs or STRs). By identifying polymorphic makers, rather than simple repeat regions as previous programs have done, iMSAT greatly increases the speed at which polymorphic MSATs that can be identified -- saving researchers precious time and money. Visit http://www.biomedcentral.com/1471-2164/15/858/abstract for the pdf article describing the utility of iMSAT and if you use the program please cite this article as: Andersen and Mills: iMSAT: a novel approach to the development of microsatellite loci using barcoded Illumina libraries. ...
