Deal with nucleotides and molecular formula
Nucleotide sequence manipulation and analysis library
Typed client for NCBI Nucleotide database (EFetch) with FASTA and GenBank format support
GenBank flat file parser for protein and nucleotide records
Nucleotide sequence manipulation tools
Display a protein/nucleotide sequence
NCBI E-utilities — federated Entrez search/fetch (PubMed/Gene/Nucleotide/…)
Nucleotide sequence manipulation and analysis library
used to manipulate and convert genetic strings from nucleotide to codon to protein
A light weighted tool to retrieve protein or nucleotide sequences based on list of ACCESSION ids from NCBI protein and nuccore database
High-performance nucleotide sequence distance calculations compiled to WebAssembly
Implementation of the Needleman–Wunsch algorithm, used in bioinformatics to align protein or nucleotide sequences.
An interactive sequence alignment viewer and editor built as a Svelte 5 component library. AliVibe provides canvas-based rendering of nucleotide and amino acid alignments with phylogenetic tree visualization, real-time editing, and multiple sequence align
Many tools allowing to analyze mass spectra
Helper that allows to query the OctoChemDB webservices
an open source bioinformatics package for retrieving, processing and analyzing the sequences and structures of biomolecules, such as proteins and nucleotides.
Sequence tracks for HiGlass
Comprehensive NCBI Database CLI tool for querying E-utilities API - Gene, PubMed, ClinVar, SRA, BLAST, and more
This is a 3-D protein structure viewer for JBrowse 2
Bioinformatics support (import/export of sequences, conversion, visualization, analysis). [See more](https://github.com/datagrok-ai/public/blob/master/packages/Bio/README.md) for details.
tools for comparing biological sequences with k-mer sketches
This plugin packages https://github.com/gmod/react-msaview for usage inside of JBrowse 2
Sequence tracks for HiGlass
Resgen flavored sequence tracks for HiGlass
Readers-writer access to individual cells of your collection!
Primitive nucleotide vocabulary for RustUse
High-performance SIMD-accelerated DNA sequence encoding supporting all IUPAC nucleotide codes
PlasCAD
Fast and correct perbase BAM/CRAM analysis.
Rust coder/decoder for Nucleotide Archive Format (NAF) files.
Ultra-fast SNP/indel-level distance calculator for core genome MLST analysis
Library for working with nucleotide and amino acid sequences
Fast search functions for finding things in Strings, Arrays and iterators.
A simple tool and library for generating random nucleotide sequences.
A library for efficient nucleotide sequence manipulation using 2-bit and 4-bit encodings
Single-binary, CLI-compatible replacement for CD-HIT utilities (cd-hit, cd-hit-est, cd-hit-2d, cd-hit-est-2d) in Rust.
a method to get the nucleotide sequence of translations done by the EMBOSS bioinformatics package program transeq.
Forage is grep for nucleotide data. With Forage, you can grep nucleotide sequences in FASTA using the IUPAC ambiguous nucleotides code. Useful for predicting PCR products.
ORF Finder is a library that with a sequence of nucletotides it finds the all the possible ORFs in the sequence. It will look for a sequence that starts with a start codon and ends with a stop codon. It will default to the beggining of the sequence if it cannot find an ORF long enought with the start codons. It will also use the end of the sequence if no stop codons are present in the sequence reading frame.
A biogem for counting small kmers for fingerprinting nucleotide sequences. See README for details.
AnNCR-SNP integrates data from various sources, allowing the user to investigate the potential effects of variants in non-coding regions of the human genome. AnNCR-SNP consists of a database containing data on all non-coding elements and two main programs: manager and finder. The manager program is responsible for creating the local data-base, and the finder program receives the user queries in order to search in the local database and retrieve information. The user can find information about various regu-latory elements, such as TFBs, open chromatin, histone modification and methyla-tion sites, information about SNPs from dbSNP and gene information from RefSeq.
Takes a GFF and genomic sequence file, constructs CDS and when given a position and alternative base will report whether this change is in a coding region and if it results in a synonymous or non-synonymous mutation.
Word correlation analysis in ranked nucleotide sequences (bioinformatics)
This is a development release. Some features are functional at this time. Genfrag allows for rapid in-silico searching of fragments cut by different restriction enzymes in large nucleotide acid databases, followed by matching specificity adapters which allow a further data reduction when looking for differential expression of genes and markers.
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