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add bioinformatics page
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‎docs/_layout/pgwrap.html‎

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</ul>
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<hr>
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<ul class="menu-list">
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{{metasection comparisons/bioinformatics "Bioinformatics"}}
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{{metasection comparisons/data_structures "Data Structures"}}
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{{metasection comparisons/performance_enhancement "Performance Enhancement"}}
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{{metasection comparisons/math Math}}

‎docs/comparisons/bioinformatics/index.md‎

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title = "Bioinformatics"
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# Bioinformatics
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The [BioJulia](https://github.com/biojulia) organization collects a lot of great packages related to bioinformatics.
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## Bio.jl is Deprecated
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Note that the [Bio.jl](https://github.com/BioJulia/Bio.jl) package is deprecated.
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In [this blogpost](https://biojulia.dev/posts/biojl/), the main developer of Bio.jl, describes where the functionality has gone:
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* Bio.Seq became [BioSequences.jl](https://github.com/BioJulia/BioSequences.jl/)
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* Bio.Align became [BioAlignments.jl](https://github.com/BioJulia/BioAlignments.jl/)
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* Bio.Intervals became [GenomicFeatures.jl](https://github.com/BioJulia/GenomicFeatures.jl/)
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* Bio.Structure became [BioStructures.jl](https://github.com/BioJulia/BioStructures.jl/)
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* Bio.Var became [GeneticVariation.jl](https://github.com/BioJulia/GeneticVariation.jl/)
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* Bio.Phylo became [Phylogenies.jl](https://github.com/BioJulia/Phylogenies.jl/)
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* Bio.Services became [BioServices.jl](https://github.com/BioJulia/BioServices.jl/)
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* Bio.Tools became [BioTools.jl](https://github.com/BioJulia/BioTools.jl/) (now archived)
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# File Parsers
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An important task in bioinformatics is parsing files in various standard formats.
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Here we list some file formats and packages with parsers:
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* [FASTA](https://en.wikipedia.org/wiki/FASTA_format) (.fas, .fasta, .fa): DNA or protein sequences without annotations
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- [FASTX](https://github.com/BioJulia/FASTX.jl)
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* [FASTQ](https://en.wikipedia.org/wiki/FASTQ_format) (.fq, .fastq): DNA sequences with quality information
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- [FASTX](https://github.com/BioJulia/FASTX.jl)
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* [GENBANK](https://en.wikipedia.org/wiki/GenBank) (.gb, .gbk): DNA or protein sequences with annotations
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- [GenomicAnnotations.jl](https://github.com/BioJulia/GenomicAnnotations.jl)
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* EMBL (.embl): DNA or protein sequences with annotations
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- [GenomicAnnotations.jl](https://github.com/BioJulia/GenomicAnnotations.jl)
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* GFF3, GFF2/GTF (.gff): Annotated genomes
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- [GenomicAnnotations.jl](https://github.com/BioJulia/GenomicAnnotations.jl)
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* [SAM](https://en.wikipedia.org/wiki/SAM_(file_format)) (.sam): Aligned DNA sequences (typically from read mapping). Text based.
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- [XAM.jl](https://github.com/BioJulia/XAM.jl)
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* [BAM](https://en.wikipedia.org/wiki/BAM_(file_format)) (.bam): Aligned DNA sequences (typically from read mapping). Binary.
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- [XAM.jl](https://github.com/BioJulia/XAM.jl)
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* PDB (.pdb): Protein 3D structure.
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- [BioStructures.jl](https://github.com/BioJulia/BioStructures.jl)
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- [MIToS](https://github.com/diegozea/MIToS.jl)
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* [mmCIF](https://en.wikipedia.org/wiki/Macromolecular_Crystallographic_Information_File): Macromolecular Crystallographic Information File (mmCIF) also known as PDBx/mmCIF is a standard text file format for representing macromolecular structure data
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- [BioStructures.jl](https://github.com/BioJulia/BioStructures.jl)
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- [MIToS](https://github.com/diegozea/MIToS.jl)
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* [MMTF](https://github.com/rcsb/mmtf): MacroMolecular Transmission Format (MMTF) is a binary encoding of biological structures.
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- [BioStructures.jl](https://github.com/BioJulia/BioStructures.jl)
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* [DSSP](https://github.com/PDB-REDO/dssp) Protein Secondary Structure
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- [ProteinSecondaryStructures.jl](https://github.com/BioJulia/ProteinSecondaryStructures.jl)
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* [STRIDE](https://webclu.bio.wzw.tum.de/stride/) Protein Secondary Structure
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- [ProteinSecondaryStructures.jl](https://github.com/BioJulia/ProteinSecondaryStructures.jl)
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* [PAF](https://github.com/slimsuite/pafscaff) (.paf) Pairwise mApping Format.
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- [PairwiseMappingFormat.jl](https://github.com/BioJulia/PairwiseMappingFormat.jl)
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* [Stockholm][https://en.wikipedia.org/wiki/Stockholm_format] (.sto, .stk, .stockholm): Stockholm format is a multiple sequence alignment format used by Pfam, Rfam and Dfam
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- [MIToS.jl](https://github.com/diegozea/MIToS.jl)
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* [A3M](https://en.wikipedia.org/wiki/FASTA_format) A2M/A3M are a family of FASTA-derived formats used for sequence alignments
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- [MIToS.jl](https://github.com/diegozea/MIToS.jl)
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* [PIR](https://www.bioinformatics.nl/tools/crab_pir.html) Multiple sequence alignment format
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- [MIToS.jl](https://github.com/diegozea/MIToS.jl)
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# Data Structures
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The basic data structures for representing DNA, RNA and protein sequences are in [BioSequences.jl](https://github.com/BioJulia/BioSequences.jl)
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# Pairwise Sequence Alignments
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A core task in bioinformatics is aligning sequences.
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This can be done with [BioAlignments.jl](https://github.com/BioJulia/BioAlignments.jl) which includes algorithms for the following pairwise alignment types:
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* GlobalAlignment: global-to-global alignment
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* SemiGlobalAlignment: local-to-global alignment
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* LocalAlignment: local-to-local alignment
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* OverlapAlignment: end-free alignment
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# Multiple Sequence Alignment (MSA)
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I'm not aware of tools in Julia to compute multiple sequence alignment, but [MIToS.jl](https://github.com/diegozea/MIToS.jl) can read the most common MSA formats: stockholm, FASTA, A3M, A2M, PIR or Raw format
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# Package descriptions
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## BioSequences.jl
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{{badge BioSequences}}
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> Biological sequences for the julia language
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[BioSequences.jl](https://github.com/BioJulia/BioSequences.jl/) BioSequences provides data types and methods for common operations with biological sequences, including DNA, RNA, and amino acid sequences.
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It can do sequence search and pattern matching in sequences, and compute simple sequence statistics.
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## BioAlignments.jl
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{{badge BioAlignments}}
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> Sequence alignment tools
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[BioAlignments.jl](https://github.com/BioJulia/BioAlignments.jl/) provides sequence alignment algorithms and data structures.
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It includes algorithms for the following pairwise alignment types:
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* GlobalAlignment: global-to-global alignment
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* SemiGlobalAlignment: local-to-global alignment
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* LocalAlignment: local-to-local alignment
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* OverlapAlignment: end-free alignment
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## GenomicFeatures.jl
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{{badge GenomicFeatures}}
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> Tools for genomic features in Julia.
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[GenomicFeatures.jl](https://github.com/BioJulia/GenomicFeatures.jl/)
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## GenomicAnnotations.jl
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{{badge GenomicAnnotations}}
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> GenomicAnnotations is a package for reading, modifying, and writing genomic annotations in the GenBank, GFF3, GFF2/GTF, and EMBL file formats.
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[GenomicAnnotations.jl](https://github.com/BioJulia/GenomicAnnotations.jl)
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## BioStructures.jl
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> A Julia package to read, write and manipulate macromolecular structures
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{{badge BioStructures}}
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[BioStructures.jl](https://github.com/BioJulia/BioStructures.jl/)
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From the package README:
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BioStructures provides functionality to read, write and manipulate
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macromolecular structures, in particular proteins.
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[Protein Data Bank](https://www.rcsb.org/pdb/home/home.do) (PDB), mmCIF and MMTF
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format files can be read in to a hierarchical data structure. Spatial
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calculations and functions to access the PDB are also provided.
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It compares favourably in terms of performance to other PDB parsers -
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see some [benchmarks online](https://github.com/jgreener64/pdb-benchmarks) - and
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should be lightweight enough to build other packages on top of.
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## GeneticVariation.jl
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{{badge GeneticVariation}}
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> Datastructures and algorithms for working with genetic variation
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[GeneticVariation.jl](https://github.com/BioJulia/GeneticVariation.jl/)
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From the package README:
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GeneticVariation provides types and methods for working with datasets of genetic variation. It provides a VCF and BCF parser, as well as methods for working with variation in sequences such as evolutionary distance computation, and counting different mutation types.
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## Phylogenies.jl
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{{badge Phylogenies}}
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> The BioJulia package for working with phylogenetic trees and geneologies.
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[Phylogenies.jl](https://github.com/BioJulia/Phylogenies.jl/)
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This looks stale.
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From the package README:
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A julia package providing an abstract type and interface for phylogenies, a concrete phylogeny type implementation, and higher-level methods for working with phylogenies.
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In development.
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## GenomeGraphs.jl
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{{badge GenomeGraphs}}
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> A modern genomics framework for julia
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[GenomeGraphs.jl](https://github.com/BioJulia/GenomeGraphs.jl)
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From the package README:
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GenomeGraphs provides a representation of sequence graphs. Such graphs represent genome assemblies and population graphs of genotypes/haplotypes and variation.
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## BioServices.jl
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{{badge BioServices}}
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> Julia interface to APIs for various bio-related web services
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[BioServices.jl](https://github.com/BioJulia/BioServices.jl/)
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## NCBIBlast.jl
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{{badge NCBIBlast}}
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> Thin wrapper around NCBI's BLAST+ CLI https://www.ncbi.nlm.nih.gov/books/NBK569856/
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[NCBIBlast.jl](https://github.com/BioJulia/NCBIBlast.jl/)
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From the package README:
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This package is a thin wrapper around the Basic Local Alignment Search Tool CLI, better known as BLAST, developed by the National Center for Biotechnology Information (NCBI).
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For now, this uses CondaPkg.jl to install BLAST+.
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## FASTX.jl
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{{badge FASTX}}
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> Parse and process FASTA and FASTQ formatted files of biological sequences.
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[FASTX](https://github.com/BioJulia/FASTX.jl)
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FASTX provides I/O and utilities for manipulating FASTA and FASTQ, formatted sequence data files.
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## XAM.jl
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{{badge XAM}}
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> Parse and process FASTA and FASTQ formatted files of biological sequences.
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[XAM.jl](https://github.com/BioJulia/XAM.jl)
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FASTX provides I/O and utilities for manipulating FASTA and FASTQ, formatted sequence data files.
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## PairwiseMappingFormat.jl
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{{badge PairwiseMappingFormat}}
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> Parser for the PAF format in bioinformatics
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[PairwiseMappingFormat.jl](https://github.com/BioJulia/PairwiseMappingFormat.jl)
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PairwiseMappingFormat.jl provide a parser for Pairwise Mapping Format (PAF) files. PAF is a simple, tab-delimited format created by programs such as minimap2.
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## ProteinSecondaryStructures.jl
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{{badge ProteinSecondaryStructures}}
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> Wrapper to protein secondary structure calculation packages
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[ProteinSecondaryStructures.jl](https://github.com/BioJulia/ProteinSecondaryStructures.jl)
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From the package README:
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This package parses [STRIDE]( http://webclu.bio.wzw.tum.de/stride/) and [DSSP](https://github.com/PDB-REDO/dssp) secondary structure prediction outputs, to make them convenient to use from Julia, particularly for the analysis of MD simulations.
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## BioMakie.jl
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{{badge BioMakie}}
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> Plotting and interface tools for biology.
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[BioMakie.jl](https://github.com/BioJulia/BioMakie.jl)
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[BioMakie.jl](https://github.com/BioJulia/BioMakie.jl) has functions to visualize
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* Protein 3D structures
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* Multiple Sequence Alignments
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## MIToS.jl
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{{badge MIToS}}
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> A Julia package to analyze protein sequences, structures, and evolutionary information
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[MIToS](https://github.com/diegozea/MIToS.jl)
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From the package README:
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MIToS provides a comprehensive suite of tools for the analysis of protein sequences and structures.
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It allows working with **Multiple Sequence Alignments (MSAs)** to obtain evolutionary information in the Julia language [1].
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In particular, it eases the analysis of coevoling position in an MSA using **Mutual Information (MI)**, a measure of covariation.
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MI-derived scores are good predictors of inter-residue contacts in a protein structure and functional sites in proteins [2,3].
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To allow such analysis, MIToS also implements several useful tools for working with protein structures, such as those available in the **Protein Data Bank (PDB)** or predicted by AlphaFold 2.
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# Star History
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{{star_history BioSequences BioAlignments GenomicFeatures BioStructures GeneticVariation Phylogenies GenomeGraphs BioServices NCBIBlast FASTX XAM PairwiseMappingFormat ProteinSecondaryStructures BioMakie MIToS}}

‎docs/utils.jl‎

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PkgInfo(pkgname="Pluto", username="fonsp", branch="main", docslink="https://plutojl.org/", codecovlink=nothing),
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PkgInfo(pkgname="Neptune", username="compleathorseplayer", branch="master", docslink=nothing),
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PkgInfo(pkgname="BonitoBook", username="SimonDanisch", branch="main", docslink="https://bonitobook.org/website/"),
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PkgInfo(pkgname="BioSequences", username="BioJulia", branch="master"),
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PkgInfo(pkgname="BioAlignments", username="BioJulia", branch="master"),
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PkgInfo(pkgname="GenomicFeatures", username="BioJulia", branch="master"),
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PkgInfo(pkgname="GenomicAnnotations", username="BioJulia", branch="master"),
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PkgInfo(pkgname="BioStructures", username="BioJulia", branch="master"),
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PkgInfo(pkgname="GeneticVariation", username="BioJulia", branch="master"),
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PkgInfo(pkgname="Phylogenies", username="BioJulia", branch="master"),
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PkgInfo(pkgname="GenomeGraphs", username="BioJulia", branch="master"),
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PkgInfo(pkgname="BioServices", username="BioJulia", branch="master"),
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PkgInfo(pkgname="NCBIBlast", username="BioJulia", branch="master", docslink=nothing),
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PkgInfo(pkgname="FASTX", username="BioJulia", branch="master"),
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PkgInfo(pkgname="XAM", username="BioJulia", branch="master"),
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PkgInfo(pkgname="PairwiseMappingFormat", username="BioJulia", branch="master"),
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PkgInfo(pkgname="ProteinSecondaryStructures", username="BioJulia", branch="master"),
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PkgInfo(pkgname="BioMakie", username="BioJulia", branch="master", docslink="https://biojulia.dev/BioMakie.jl/dev/"),
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PkgInfo(pkgname="MIToS", username="diegozea", branch="master"),
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]
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function get_pkginfo(pkgname)

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