Search Results for "fasta"
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Showing 80 open source projects for "fasta"
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Prokka
Rapid prokaryotic genome annotation
Prokka is a command-line software tool for rapid annotation of prokaryotic genomes (bacteria and archaea). Given a FASTA file of contigs, it predicts genes, rRNAs, tRNAs, and other functional elements, then assigns functions by comparing to reference protein databases and HMM profiles. It outputs GenBank, GFF, and other formats compatible with downstream tools and genome browsers. Prokka handles common complications—overlapping ORFs, frameshifts, alternate start codons—while providing customizable databases so researchers can bias domain or strain-specific annotations. ... -
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PLEK
predictor of long non-coding RNAs and mRNAs based on k-mer scheme
...Download PLEK.1.2.tar.gz from https://sourceforge.net/projects/plek/files/ and decompress it. $ tar zvxf PLEK.1.2.tar.gz 2. Compile PLEK. $ cd PLEK.1.2 $ python PLEK_setup.py USAGE python PLEK.py -fasta fasta_file -out output_file -thread number_of_threads -minlength min_length_of_sequence -isoutmsg 0_or_1 -isrmtempfile 0_or_1 Examples: 1. $ python PLEK.py -fasta PLEK_test.fa -out predicted -thread 10 2. $ python PLEK.py -fasta PLEK_test.fa -out predicted -thread 10 -minlength 150 We upgraded PLEK to PLEKv2.: https://doi.org/10.1186/s12864-024-10662-y Aimin Li, Haotian Zhou, Siqi Xiong, et al. ... -
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PLEKv2
PLEKv2: predicting lncRNAs and mRNAs
PLEKv2: predicting lncRNAs and mRNAs based on intrinsic sequence features and the Coding-Net model INSTALLATION ------------- We upgraded PLEK to PLEKv2. All you need is RNA sequences (fasta file). Steps: 1. Download PLEK.2.1.tar.gz from * and decompress it. $ tar zvxf PLEK.2.1.tar.gz 2. Compile PLEK2.1 $ cd PLEK2.1 3. decompress Coding_Net_kmer6_orf.h5.bz2 model $ bunzip2 Coding_Net_kmer6_orf.h5.bz2 4. decompress Coding_Net_kmer6_orf_Arabidopsis.h5.bz2 model $ bunzip2 Coding_Net_kmer6_orf_Arabidopsis.h5.bz2 USAGE Python PLEK2.py -i fasta_file -m model(ve: vertebrate , pl: plant) Examples: $ python PLEK2.py -i test.fasta -m ve Aimin Li, Haotian Zhou, Siqi Xiong, Junhuai Li, Saurav Mallik, Rong Fei, Yajun Liu, Hongfang Zhou, Xiaofan Wang, Xinhong Hei, Lei Wang. ... -
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Fasta-browser
Fasta-browser
Fasta-browser https://fasta.top -
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InterMine
A powerful open source data warehouse system
InterMine is an open-source data warehouse system tailored for the integration and analysis of complex biological data. It enables researchers to create databases from diverse data sources and provides sophisticated web query tools for data exploration. -
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sRNAWorkbench
The UEA sRNA Workbench
A suite of tools for analysing small RNA (sRNA) data from Next Generation Sequencing devices. Including expression profiling of known mirco RNA (miRNA), identification of novel miRNA in deep-sequencing data and identification of other interesting landmarks within high-throughput genetic data -
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PAN2HGENE, a computational tool that allows identification of gene products missing from the original genome sequence, with automated comparative analysis for both complete and draft genomes, can be used to address this limitation. In this study, PAN2HGENE was used to identify new products, resulting in altering the alpha value behavior in the pangenome without altering the original genomic sequence. Our findings indicate that this tool represents an efficient alternative for comparative...
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miRSim
Seed-based RNA-Seq Simulator
The miRSim tool can generate the synthetic RNA-Seq data in standard fastq/fasta format by utilizing the sequence-specific properties (i.e., seed and xseed (remaining part of the sequence after removing seed)). Additionally, miRSim also generates the ground truth in CSV format that provides information about genomic location, CIGAR string, sequence, and expression counts. -
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...SimulaTE will greatly aid in evaluating the suitability of different approaches for estimating TE abundance within populations and to test whether given genomic resources, such as a reference genome or a TE database (a fasta file containing consensus sequences of TEs), are suitable for TE identification. Manual https://sourceforge.net/p/simulates/wiki/Home/#manual Walkthrough https://sourceforge.net/p/simulates/wiki/Home/#walkthrough Validation https://sourceforge.net/p/simulates/wiki/Home/#validation
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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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fas2svg
Visualize genetic code structure from fasta file.
Generate svg file from fasta file. -
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FastaTools
Performs several operations to Fasta protein databases
FastaTools performs several operations to Fasta protein databases. For more information, you can have a look at the README.md file in the source code tree: https://sourceforge.net/p/lp-csic-uab/fastatools/code/ci/default/tree/README.md Or you can download the Documentation an Tutorial PDF file in the Files section: https://sourceforge.net/projects/fastatools.lp-csic-uab.p/files/FastaTools%20Documentation%20and%20Tutorials.pdf - Gallardo, Ó., Ovelleiro, D., Gay, M., Carrascal, M., & Abian, J. (2014). ... -
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SVPhylA
SVPhylA: Sequence Vectorization for Phylogenetic Analyses
SVPhylA is a python tool for the calculation of several alignment-free distances for phylogenetics analysis from the most popular alignment-free approaches. Such alignment-free methods basically encode DNA and protein sequences (fasta files) into numerical vectors allowing the calculation of alignment-free distances which may be combined into a consensus/compromise matrix by using algorithms like DISTATIS based on Multidimensional Scaling (MSD), Lineal Principal Component Analysis (PCA) and PCA-Kernel (non-lineal). In addition, genetic distances derived can be either combined between them or with the alignment-free distances. ... -
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RELEASE NOTE: Get raxmlGUI 2.0 at the NEW PROJECT LOCATION: https://antonellilab.github.io/raxmlGUI/ raxmlGUI is a graphical user interface to RAxML, one of the most popular and widely used software for phylogenetic inference using maximum likelihood. A userfriendly graphical front-end for phylogenetic analyses using RAxML (Stamatakis, 2006). Please cite: Silvestro, Michalak (2012) - raxmlGUI: a graphical front-end for RAxML. Organisms Diversity and Evolution 12, 335-337. DOI:...
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ENPG
A tool to extract potential neuropeptides from protein sequence data.
...The currently available version is dedicated to extract peptides that shows the structural hallmarks of cnidarian neuropeptides (C-terminal amidation, proline at N-terminus and pyro-Glutamate). The output FASTA file can be used as a target data set for peptide-spectrum matching to effectively narrow search space for highly sensitive peptide identifications. -
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lemonade_assemble
Specialized sequence assembly tools
...Assembly of pooled BACs from PacBIO reads. 2. Polymorphic genome assembly 3. Processing of Trinity transcriptomes 4. Modified versions of other people's code used in any of the above. 5. Fasta processing and miscellaneous programs and scripts. Documentation is rudimentary or nonexistant. -
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selectseq
Get specific sequences from a FASTA or FASTQ file.
A command-line utility to manipulate biological sequences from a FASTA or FASTQ file. It can, given a list of identifiers, get only a subset of the sequences (or their complement, i.e., sequences NOT in the list). Can also get sequence number N only. Compressed sequences files are supported if readable by zcat. -
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PROPAB
PROPensity for Alpha and Beta
PROPAB: Computation of Propensities and Other Properties from Segments of 3D structure of Proteins Authors: Rifat Nawaz UL Islam1, Chittran Roy2, Parth Sarthi Sen Gupta3, Debanjan Mitra2, Sahini Banerjee4 and Amal Kumar Bandyopadhyay2* 1Department of Zoology, The University of Burdwan, West Bengal, 713104, India 2Department of Biotechnology, The University of Burdwan, West Bengal, 713104, India 3Department of Chemistry, IISER, Berhampur, Odisha, 760010, India 4Department of... -
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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.
