Search Results for "dna sequence"
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Showing 150 open source projects for "dna sequence"
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Finding DNA Repeats by RFRE
RFRE is a tool to find DNA repeats (tandem and short)
A tool to FIND DNA REPEATS (tandem and short): RFRE is a mini tool to search for the repeated DNA sequences (SHORT REPEATS OR TANDEM REPEATS) characters by using the regular expression language (VB script). The Metacharcter and their behaviours in the context of regular expressions are the main methods to identify the different searched patterns and by different combination of Metacharcter, the programmed tool can search and detect the pattern of DNA sequence. Repeater Finder... -
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binocular
Binocular segmentation of whole-genome DNA sequence data
Segmentation-based detection of copy-number alterations and allelic imbalances in whole-genome DNA sequence data. -
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proSeq
ProSeq is a GUI program to edit and analyse DNA polymorphism datasets
ProSeq ('Processor of sequences') is a package including GUI and command line programs to process and analyse DNA polymorphism data. It allows one to open and save sequence data in over a dozen file formats (and convert between these formats). It shows sequence alignments in a graphical window and allows the user to edit, manipulate and analyse sequences in various ways. Sequence analyses include DNA polymorphism and basic phylogenetic reconstruction (NJ only). The program can also run... -
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XLibraryDisplay
A sequence analysis tool for protein engineering
XLibraryDisplay is an intuitive sequence analysis program optimized for protein engineering. It is ideal for all directed evolution platforms including phage, ribosome, and yeast display. Analysis can be quickly done on hundreds to thousands of sequences. Best suited for Sanger sequencing. Requirements: Microsoft Windows XP, 7, 8, or 10 and Excel 2007, 2010, 2013, or 2016 Described in Stafford et al JCIM 2014: http://pubs.acs.org/doi/abs/10.1021/ci500362s -
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BioBytes PairSync
A Bioinformatics Tool for Basic Information Retrieval
This GUI app allows users to input biological sequences, either manually or by loading from a file. It supports DNA, RNA, and Protein sequences. Users can retrieve various information about the input sequence, such as nucleotide or amino acid frequency, GC content, reverse complement, transcription, translation, amino acid molecular weight, isoelectric point, and open reading frames. Users can save the output information to a text file and clear the output section for a clean slate... -
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janda
structural variant detector
Janda is a tool to detect structural variants in whole-genome DNA sequence data. It identifies structural variants (deletions, duplications, translocations, and inversions) using anomalously mapped pair reads and realigning potential junction reads. -
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est-sfs
Estimate the unfolded site frequency spectrum and ancestral states
est-sfs implements a maximum likelihood method to infer the unfolded site frequency spectrum (the uSFS) and ancestral state probabilities for DNA sequence data. The uSFS is a vector of counts of nucleotide sites with x derived allele copies in a sample of gene copies from a population. est-sfs infers the uSFS and ancestral state probabilities at polymorphic sites in a focal species using information from up to three outgroup species. Three models of nucleotide substitution have been implemented... -
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Peptide Pattern Recognition
Software for non-alignment based analysis of DNA and protein sequences
Software for analysis, grouping and functional prediction of DNA and protein sequences as described in: Busk P.K. (2017). Peptide Pattern Recognition for high-throughput protein sequence analysis and clustering. BioRxiv. doi: https://doi.org/10.1101/181917. Busk P.K. and Lange L. (2013). Function-based classification of carbohydrate-active enzymes by recognition of short, conserved peptide motifs. Appl Environ Microbiol. 79(11), 3380-91. Busk P.K. Lange M. Pilgaard B. and Lange L. (2014... -
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Design PCR primers from DNA sequence. Widely used (190k Google hits for "primer3"). From mispriming libraries to sequence quality data to the generation of internal oligos, primer3 does it. C&perl. Developers/testers/documenters needed.
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ASGARD
Metabolic reconstruction from DNA or protein sequences.
ASGARD is software for metabolic pathway reconstruction, but it can also generate other types of biological sequence annotation (EC and GO numbers, BLAST reports). This program is intended to be run in UNIX-like systems, and supports SGE or PBS. -
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Citrus
Citrus: Editing HiC data for de novo genome assembly
juicer and 3D-DNA are two tools that re-arranges HiC data (xxx.hic format) and splits/re-orders super-scaffold data (xxx.assembly) to improve de novo genome assembly. Juicebox was specifically designed to tune or adjust genomic sequences based on HiC data. However, the current Juicebox version does not have a function to save updated HiC data and to summarize chromosome sequences. Thus, we created Citrus which can edit super-scaffolds according to chromatin conformation data captured in xxx.hic... -
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gendasm
Generic Code-Seeking Diassembler with Fuzzy-Function Analyzer
GenDasm is a Generic Code-Seeking Diassembler engine. It allows you to enter known starting vectors for a given code image for the micro. It will disassemble the code and follow through branches to assist in the separation of code and data. Its included Fuzzy Function Analyzer companion uses a DNA Sequence Alignment Algorithm to locate similar code in multiple binaries to facilitate reverse-engineering and/or code recovery. The original purpose of the Fuzzy Function Analyzer was to assist... -
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GMATA software for Genomic SSR marker
Genome-wide Microsatellite Analyzing Toward Application: GMATA
What is software GMATA v21 Genome-wide Microsatellite Analyzing Toward Application (GMATA) is a software for Simple Sequence Repeats (SSR) analyses, and SSR marker designing and mapping in any DNA sequences. It has the following functions: 1. SSR mining; 2. Statistical analysis and plotting; 3. SSR loci graphic viewing; 4. Marker designing; 5. Electronic mapping and marker transferability investigation. GMATA is accurate, sensitive and fast. It was designed to process large genomic... -
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m6811dis
M6811 Code-Seeking Disassembler
The M6811 Code-Seeking Disassembler is a command-line tool that lets you enter known starting vectors for a given code image for the 6811 micro. It will disassemble the code and follow through branches to assist in the separation of code and data. Its companion Fuzzy Function Analyzer uses DNA Sequence Alignment Algorithms to locate similar code in multiple binaries, facilitating reverse-engineering. Originally written to analyze code from GM automotive engine controllers, but is useful... -
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GenSeed-HMM
Progressive assembly tool using DNA, protein or profile HMMs as seeds.
... The first seed is provided by the user, and can be a piece of DNA or protein sequence, or an HMM profile, for increased sensitivity. This program depends on BLAST+ or hmmsearch and a number of third-party support tools (EMBOSS' transeq and splitter, bowtie, 454's sfffile and sffinfo). Which tools will be mandatory depends on the kind of seed and assembler used. Assemblers currently supported include CAP3, Newbler, SOAPdenovo, Velvet, and Abyss. -
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GapFiller
A de novo local assembler for paired reads
GapFiller is a seed-and-extend local assembler to fill the gap within paired reads. It can be used for both DNA and RNA and it has been tested on Illumina data. GapFiller can be used whenever a sequence is to be assembled starting from reads lying on its ends, provided a loose estimate of sequence length. -
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A fully developed set of DNA sequence assembly (Gap4 and Gap5), editing and analysis tools (Spin) for Unix, Linux, MacOSX and MS Windows.
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TARGT pipeline
Targeted Analysis of sequence Reads for GenoTyping of HLA/MHC genes
The 'TARGT' pipeline for Targeted Analysis of sequencing Reads for GenoTyping can be used for genotyping of MHC/HLA genes (or other genomic regions) from ancient and modern shotgun sequence data with moderate to low sequence coverage. The pipeline consists of a main bash script that calls the different steps of the pipeline and can either be called directly or submitted to a cluster queue system, as well as additional sub-scripts and files, that are required to perform the different steps... -
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An alignment-free standalone tool with interactive graphical user interface for DNA sequence comparison and analysis
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seqdiva
SeqDivA:Sequence Diversity Analysis
Sequence Diversity Analysis - SeqDivA version 1.0 is a python-based tool with a friendly GUI designed for Linux and Mac OS. Utility: Run alignment algorithms (water, needle, and blast) to compare all-vs.-all protein, DNA, and RNA sequences. SeqDivA provides similarity, identity, and bit-score matrixes and dot plots to explore/illustrate the diversity (homology degree) of the sequences, enabling the delimitation of the twilight zone. Installation: - Download SeqDivA... -
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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... -
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TI2BioP allows mainly the calculation of topological indices (spectral moments) derived from inferred and artificial 2D structures of DNA, RNA and proteins being possible to carry out a structure-function correlation irrespective of sequence alignments. TI2BioP version 3.0 is a python platform with a graphical interface designed for Windows, Linux and Mac OS.
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GMOL
A tool for 3D genome structure visualization
GMOL is an application designed to visualize genome structure in 3D. It allows users to view the genome structure at multiple scales, including: global, chromosome, loci, fiber, nucleosome, and nucleotide. This software was built upon the pre-existing Jmol package by Prof. Cheng's group. The software is developed in Prof. Jianlin Cheng's Bioinformatics, Data Mining and Machine Learning Laboratory in the Computer Science Department at the University of Missouri - Columbia, USA. The project... -
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PWMScan
A Web-based genome-wide Position Weight Matrix (PWM) Scanner
PWMScan is used to scan a position weight matrix (PWM) against a genome or, in general, a large set of DNA sequences. The PWM is the most commonly used mathematical model to describe the DNA binding specificity of a transcription factor (TF). A PWM contains scores for each base at each position of the binding site. The TF binding score for a given k-mer sequence is then obtained by simply adding up the base-specific scores at respective positions of the binding site. PWMScan takes as input... -
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spark-msna
Algorithm on Spark for aligning multiple similar DNA/RNA sequences
The algorithm uses suffix tree for identifying common substrings and uses a modified Needleman-Wunsch algorithm for pairwise alignments. In order to improve the efficiency of pairwise alignments, an unsupervised learning based on clustering technique is used to create a knowledge base to guide them.