Search Results for "fasta" - Page 3
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Showing 102 open source projects for "fasta"
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AlignMerger
A tool for merging two large multiple sequence alignments
AlignMerger is useful to merge two sets of multiple sequence alignments (MSA). It can greatly reduce the computational time needed to construct a MSA, compare to others commonly used MSA tools. Inputs required for the tool are two MSAs in FASTA format and output of the tool is a merged MSA in FASTA format. -
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Sequencia
Protein Primary Sequnece Analysis
...JAVA, BIOJAVA were used under Platform Independent architecture. The Tool includes Properties of being offline where result can be stored in Text Format, here we can paste more than one sequence and also upload FASTA file to compute Parameters. -
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Flexbar
flexible barcode and adapter removal for sequencing platforms
...It demultiplexes barcoded runs and removes adapter sequences. Moreover, trimming and filtering features are provided. Flexbar supports next-generation sequencing data in fasta and fastq format, e.g. from the Illumina platform. Reference: Matthias Dodt, Johannes T. Roehr, Rina Ahmed, Christoph Dieterich: Flexbar — flexible barcode and adapter processing for next-generation sequencing platforms. Biology 2012, 1(3):895-905. -
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PHYSICO2
PHYSICO2: Software for Computation of Properties of Protein Sequences
Program: PHYSICO2: An UNIX based Standalone Procedure for Computation of Physicochemical, Window-dependent and Substitution Based Evolutionary Properties of Protein Sequences along with Automated Block Preparation Tools, Version 2 . Version:--v2.0 - improved version of PHYSICO: Gupta et al Bioinformation, 10(2), 105-107, 2014 Author:c)--Shyamashree Banerjee1+, Parth Sarthi Sen Gupta1+, Arnab Nayek1+, Sunit Das1, Vishma Pratap Sur1, Pratyay Seth1, Rifat Nawaz Ul Islam1, & Amal K... -
MongoDB Atlas runs apps anywhereMongoDB Atlas gives you the freedom to build and run modern applications anywhere—across AWS, Azure, and Google Cloud. With global availability in over 115 regions, Atlas lets you deploy close to your users, meet compliance needs, and scale with confidence across any geography.
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newDNA-Prot
dna binding protein predict soft
...In windows system,open my computer->all programs->Accessories->Windows Powershell->Windows Powershell.And in the Windows Powershell, we must be carried out as an adminstrator.Then in the command line of windows Powershell, we need input the Powershell script to execuate permissions:"Set-ExecutionPolicy Unrestricted". INPUT FILE: sequence_file in fasta format. One sequence per file. -
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SuRankCo
Supervised Ranking of Contigs in de novo Assemblies
...Renard (http://www.biomedcentral.com/1471-2105/16/240/abstract) PLEASE NOTE, it is recommended to read the paper and the readme.txt file before using SuRankCo. Update Jun2015: * Minor changes to enable BAM support. Update Feb2014: * Added support for FASTA/SAM assemblies in addition to ACE/FASTQ(QUAL). NOTE: features of FASTA/SAM assemblies do not include BaseCount, BaseSeqmentCount and ContigQualities yet. -
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Hadoop-BAM is a Java library for the manipulation of files in common bioinformatics formats using the Hadoop MapReduce framework with the Picard SAM JDK, and command line tools similar to SAMtools. The file formats currently supported are BAM, SAM, FASTQ, FASTA, QSEQ, BCF, and VCF. For a longer high-level description of Hadoop-BAM, refer to the article "Hadoop-BAM: directly manipulating next generation sequencing data in the cloud" in Bioinformatics Volume 28 Issue 6 pp. 876-877, available online at: http://dx.doi.org/10.1093/bioinformatics/bts054 Note that the library part of Hadoop-BAM is mainly for developers with experience in using Hadoop. ...
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SSC
Spacer Scoring for CRISPR
SSC is a tool for predicting sgRNA efficiency from spacer sequences. It supports the applications of optimizing sgRNA libraries in CRISPR/Cas9 knockout or CRISPR/dCas9 inhibition/activation screens. -
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UniPyRange
Tool to fetch protein/DNA truncation constructs from Uniprot DB
Very simple python script which saves you the pains of counting the amino acids/DNA bases in fasta files from the Uniprot and NCBI RefSeq Database (1, 2). Lets say you want the amino acid sequence of range 128-387 from a 1000 amino acid protein - this script will help you to avoid counting mistakes by just showing you the specified sequence in amino acids and coding DNA base pairs (ideal for amplification primer design) of a specified Uniprot ID -
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SimplyTheBlast
Blast query sequences on a set of fasta formatted genomes
SimplyTheBlast: a small perl tool to build genes presence/absence matrices over a set of Fasta formatted genomes. This code requires: Bio::SeqIO; Bio::Perl; Bio::Tools::Run::StandAloneBlast; Bio::Seq; Bio::Tools::Blast; Bio::DB::GenBank; Bio::DB::WebDBSeqI; and BLAST 2.2.28 (blastall and formatcmd) installed and reachable from your command line Usage: perl SimplyTheBlast-Align.pl <fasta formatted seeds file> <path to genomes folder> <Alignment length threshold in %> <Alignment identity threshold in %> OR Usage: perl SimplyTheBlast-Evalue.pl <fasta formatted seeds file> <path to genomes folder> <Evalue threshold> Genomes files names must end with *.faa Output files: TABULAR_FBH_OUTPUT.xls is an Excel readable file with the identifier of the best hits found TABULAR_FBH_OUTPUT.csv is a file with the number of the best hits found query_n* files are fasta formatted files with the sequences of the best hits found bugs /comments: marco.fondi@unifi.it -
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Just_Annotate_My_Genome
Comprehensively annotate your non-model species genome.
Uses an existing exonerate output or just predicted proteins (e.g. from Transdecoder or just a FASTA file) to prepare gene prediction inputs for Augustus, SNAP and geneid. Exonerate is run (enabled via AAT) if it is not provided. GTF file is produced to judge quality of annotation. Sorts out high quality alignments from those that don't meet the criteria. -
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mitoMaker
mitoMaker - a mitochondria assembly and annotation script
mitoMaker is a pipeline script developed to simplify the assembly and automatic annotation of mitochondrial genomes, based on raw NGS reads and an optional target reference. mitoMaker calls well known assemblers and algorithms, such as SOAPdenovo, MIRA and blast+ and parses their results providing easily readable outputs, such as FASTA, GENBANK, SEQUIN, PNG and others. General pipeline: 1-iterative De Novo assembly, with different k-mer values, trying to assemble a build that matches a target mitochondrial genome given. 2-searches for all mitochondrial gene features and circularization. 3-stores the best result found. 4-uses the best assembly as backbone for a reference based assembly, using MIRA and MITObim, trying to extend the mitogenome and close gaps. 5-annotates the best assembly, identifying the start and end position of each and every feature. 6-creates a folder with all the results (PNG, GENBANK, FASTA, SEQUIN, CAF, MAF and a stats logfile). -
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Parapipe
A Perl tool for orthologous sequences detection across a genomes set
...This tool iteratively launches Inparanoid (http://inparanoid.sbc.su.se/cgi-bin/index.cgi) and Multiparanoid (http://multiparanoid.sbc.su.se/) softwares on a set of genomes and outputs FASTA sequences of core, accessory and uniques genomes. -
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AFSM_seq
a simple and rapid method for genome-wide SNP and methylation site
Reference based analysis 1.Filter the raw reads obtained from Illumina Raw Data (paired-ends)according to your desired stringency, to produce a set of high-quality (HQ) sequences in fastq format. 2.Lignment reads (HQ, Fastq format) against Barcode file (Fasta format) using scanAP program. 3.Trim barcodes and filter paired-ends using trim_seq.pl. Classified paired-ends using fltfastq2pe.pl. to produce output “R1.trim.pair.fastq” and “R2.trim.pair.fastq”. 4.The filtered sequence reads were aligned to the reference genome using the Bowtie2, allowing a maximum of four mismatches and one gap of up to 3 bp. ... -
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NGSimple
NGS - Next-Generation Sequencing sIMulation PipeLinE
This pipeline, mainly written in perl is designed to simulate NGS parameters (illumina sequencing type, read length, insert size and coverage) based on a given reference, and give a report to choose the best parameter combination that could contribute to a good assembly. simulation.pl generates simulated reads from a reference in fasta format. It's recommended to start with a short reference (~5M bases), in case that the number of generated reads is too large for assembly. input: reference + parameter output: ./1.fastq/reads.fastq assemly.pl assemble the reads (./1.fastq/reads.fastq) from those designed libraries to assemblies. based on the parameters specified in CONFIG file. ... -
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FIAP
Fully Integrated Annotation Pipeline
...This feature is extremely valuable because it allows users to add a personal “flavor” to the annotation and optimize the process for a specific bacterial genome. FIAP can annotate single and multiple sequences, which allows users to annotate, for example, draft genome contigs or different genomes concatenated in multi-fasta file in a single step. FIAP works on all UNIX-like operating systems (tested on Ubuntu 14.04 LTS and Mac OS 10.9.4). -
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WaMoFi
Wa[velet] Mo[tif] Fi[nder]
...Please use: R 3.1.0 and Matlab 2014 How to use: Just replace the directory and files In the head of the WaMoFi.m script. Then, run it in a matlab console. --dataset: your data set in a fasta file --labels: a file with the label/class per line --percTest: how much of the test will be used for finding the motifs?. 0.7 means the 70% of the sequences in each class are used to find the motifs, whereas, the 30% are used to validate those motifs. --outDir: directory where do you want the output --SourceDir: where the WaMoFi files are stored in your machine. ... -
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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, Illumina call files) * work with genetic maps ... -
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x2fasta
Tools for reformatting common sequence formats into fasta
A collection of tools to transform common biosequence formats (e.g. EMBL, SWISS-PROT, UniProtKB, GenBank and RefSeq) into the fasta sequence format. -
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Genome Microsatellite Analyzing Tool
GMATO : Microsatellite Analyzing Tool for Huge Genome at any size
...Genome-wide Microsatellite Analyzing Tool (GMATo) is a novel powerful program for faster SSR mining at any length, any size,and comprehensive statistical analysis at genome aspect, especially designed for huge genome based on Perl scripts. Only one input file is required which contains DNA sequences in raw fasta format and output files in tabular format list all SSR loci information and statistical distribution at four biologist interested classifications. GMATo also has easy and graphical user interface scripted in Java and command line interface in Perl, either running in Windows, Linux and Mac etc. platforms with easily customized parameters control for biologists and bio-informatician. ... -
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Bioinformatic tools for analyzing an orfeome using translated ORFs and compares each ORF to the provided Orfeome/Proteome. Our script uses NCBI BLAST run locally and MySQL as the main engines in a new and interisting way. It is designed specifically for Poxvirus genomes, and provides the VACV-COP nomenclature and Cowpox Ortholog groups per each ORF. The BLAST stats are generated when compared to the Proteome you provide. It can be easily adapted for other genomes.
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OrthoRBH
Rapidly identify orthologous cDNA sequences in related species
...It performs batch blast searches, so it is ideal for large multi-gene families. After collecting candidate sequences, it performs sequence alignment and deposits sequences into a fasta sequence file for downstream molecular evolutionary analysis. -
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SOAPindel2
SOAPindel2 focusing on calling indels from the next-generation p
Requirements SOAPindel2 needs two input data sources: The reference sequence file used to align the reads. It must be in Fasta format. The files with read-alignments. SOAPindel2 accepts only Indexed BAM formats as input. Users can use the tools/soap2sam.cc to convert SOAP format to SAM format and use samtools convert SAM to indexed BAM. SOAPindel2 can guess the library insert sizes by itself. Sequencing platform:Theoretically, SOAPindel2 is designed for all paired-end sequencing data because it doesn’t consider any qualities for now. ... -
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primeScaff is intended to automate the sometimes tedious process of manually designing specific primer pairs around gaps of genomic scaffolds and speedup the genome finishing stage of a genome sequencing project. It incorporates de-novo repeat finding using RECON to avoid as much as possible designing primers in repetitive regions and offers the possibility to easily fine-tune the primer design options using primer3. It outputs the repeat, gap and primer annotations in gff2 and gff3 to...
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ligth-genome-view
small genome viewer local wxWidget c++
...I am a newbie in bioinformatics. Hope this will give people help when build bio-GUI project using c++. This software is used to view genome including many type files,like bed,gff,gtf,vcf,fasta,bam.
