Search Results for "fasta" - Page 4
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Showing 102 open source projects for "fasta"
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GenOO-HTS
A Modern Perl Framework for High Throughput Sequencing analysis
GenOO-HTS [jee-noo] is an open-source; object-oriented Perl framework specifically developed for the design of High Throughput Sequencing (HTS) analysis tools. The primary aim of GenOO-HTS is to make simple HTS analyses easy and complicated analyses possible. GenOO-HTS models biological entities into Perl objects and provides relevant attributes and methods that allow for the manipulation of high throughput sequencing data. Using GenOO-HTS as a core development module reduces the overhead... -
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GAAS (Genome relative Abundance and Average Size) is a bioinformatic tool to calculate accurate community composition and average genome size in metagenomes by using BLAST, advanced parsing of hits and correction of genome length bias.
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NeedlemanWunsch
Fast global sequence alignment for the masses!
MOVED TO GITHUB: https://github.com/noporpoise/seq-align Global optimal sequence alignment using the Needleman-Wunsch algorithm. Aligns DNA, RNA, protein sequence and more! See our sister project local alignment using Smith-Waterman: http://sourceforge.net/projects/smithwaterman/ -
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CS-AMPPred
The Cysteine-Stabilized Antimicrobial Peptides Predictor
This program reads a fasta file specified by -i option, then, converts it to SVM Light format, further runs the classification module of SVM Light and then evaluate the predictions. The support vector machine models were based on 310 antimicrobial peptide sequences extracted from antimicrobial peptides database and 310 non-antimicrobial peptide sequences extracted from protein data bank. -
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...Additional screencast tutorial videos are provided to describe how to install these programs as well as examples for executing both De-MetaST and De-MetaST-BLAST. ++++++++++++++++++++++++++++ De-MetaST = metagenome search tool -output: FASTA file of retrieved amplicons -tutorial video: install_De-MetaST.mp4 De-MetaST-BLAST = metagenome search tool + BLAST -output: (1)FASTA file of retrieved amplicons and (2)TXT file of predicted functions for each amplicon -tutorial videos: (1)install_local_BLAST.mp4 and (2)install_De-MetaST-BLAST.mp4 ++++++++++++++++++++++++++++ All files must first be uncompressed before use. ...
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Swift Sequence Alignment Program
GPU-based DNA sequence alignment program using Smith-Waterman
Swift is a DNA sequence alignment program that produces gapped alignment using the Smith-Waterman algorithm. It takes in a query file (FASTA format) and a reference file (FASTA format) as input. It outputs the reference name, read name, gapped alignment, alignment score, alignment start and end positions, and alignment length. I gave a talk on Swift in the GPU Technology Conference 2012. The talk can be accessed at http://www.gputechconf.com/gtcnew/on-demand-GTC.php?... -
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Javamony
A Student's Approach to the Phylogenetic Problem
Based on the not-so-successful Pysimony (https://sourceforge.net/projects/pysimony/), the same determined student takes another go at the phylogenetic problem. Javamony is invoked as follows: java -jar Javamony.jar [input.fasta] [random / stepwise (starting tree)] [# of bootstraps] [outgroup taxon #1] [outgroup taxon #2] ... Not meant as a competitive phylogenetic inference program, Javamony is an opportunity for me to acquire the Java language while learning to address and solve... -
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Pysimony
A Pythonic Implementation of Parsimony Inference of Phylogeny
UPDATE: After some bug fixes, I've ditched Pysimony for Javamony: https://sourceforge.net/projects/javamony/ Given Python's beauty, I know that someday I will have to finish Pysimony. A student's first attempt at a phylogenetic inference program, written in the simplistic yet elegant Python. Pysimony reads a FASTA file (only ATGC accepted) specified as its only argument. Basic testing has shown that it is slow, inaccurate and most definitely inefficient. An unlikely-to-be-the-most-parsimonious tree is printed upon completion in basic Newick tree format. As all parts of the program are the original work of a beginner programmer, this may represent one of the worst approaches to solving the phylogenetic problem. ... -
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CRUMp
A probabilistic prediction system of protein phosphorylation sites
CRUMp is based on a kernel-based learning method called Classification Relevance Units Machine (CRUM). Given an input set of protein sequences in FASTA format, the system outputs the position, residue type (S, T, or Y), and the estimated probability of each tested site being phosphorylatable. Latest downloadable files: - crump-0.2.0.tar.gz: CRUMp GNU Octave package - crump-0.2.0.zip: CRUMp MATLAB script - crumptestset.fasta: A testing dataset in FASTA format. The sequence headers list the accession number of the protein sequence and the position numbers of known phosphorylation sites. ... -
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SmithWaterman
Fast local sequence alignment for the masses!
MOVED TO GITHUB: https://github.com/noporpoise/seq-align An implementation of the Smith-Waterman local sequence alignment algorithm. See our sister project global alignment using Needleman-Wunsch: http://sourceforge.net/projects/needlemanwunsch/ -
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FFP (Feature frequency profile) is an alignment free comparison tool for phylogenetic analysis and text comparison. It can be applied to nucleotide sequences, complete genomes, proteomes and even used for text comparison.
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MSDB
Microsatellite Search and Building Database
MSDB (Microsatellite Search and Building Database) is specially designed to offer you a user-friendly interface for finding microsatellite markers, their exact position and frequency of occurrence from genomic sequence. MSDB can accept large number of sequences in GenBank, FASTA and EMBL formats as input and large number of motifs can be searched simultaneously. The program not only can search pure microsatellite but also can search compound and complex microsatellite. The outputs are Microsoft Excel statistics and SQLite database file which is convenient for analysis and classification of microsatellites. ... -
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A set of command-line utilities for annotating and manipulating DNA sequences in FASTA format. Generate restriction fragments, ORF's, translations, reverse complement, etc. . - and tie it all together with Unix pipes for complete virtual cloning.
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Filters DNA sequence files based on length, N-content, and occurrence of a QC reference sequence (fasta or fasta+qual formats)
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These scripts written in Python allow you to convert fasta files into multifasta file and vice versa.
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fast indexing and retrieval of fasta records from flat file databases.
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This is a utility to convert a set of fasta formatted sequences along with output from ELAND or SOAP (and other next generation sequence alignment in due time) to make them viewable using eagleview.
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PKSIIIpred is the type III polyketide synthase prediction server based on SVM .Users can submit their protein sequences in fasta format to predict whether the given protein sequence belongs to type III Polyketide synthase or not.
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TrypC was developed for digesting protein sequences into peptides using fully, semi, and nontryptic cleavage conditions. Associated libraries allow direct loading of data from FASTA files.
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BushMan is a web interface and a quality assurance tool for biological sequence assembly. It is a small application that helps process chromatograms, and it assembles using Phred and Phrap. It produces a FASTA formatted consensus sequence.
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The purpose of the project is moving large-size of biological database and FASTA computation onto wide area network by leveraging distributed computation-enabled storage developed for the field of logistical network.
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RepeatFinder is a command line tool for generating non-overlapping matches of microsatellite DNA from FASTA format code.
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POSA (Perl Objects for Sequence Analysis) provides an easy-to-use perl interface to handling raw ABI sequence trace files. For example: fasta can be extracted, sequence contigs can be build and putative SNPs and SBE primers can be easily generated.
