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‎docs/comparisons/bioinformatics/index.md‎

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@@ -26,40 +26,23 @@ In [this blogpost](https://biojulia.dev/posts/biojl/), the main developer of Bio
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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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| Format | Extensions | Description | Packages |
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|-----------------------------------------------------------------------------------------|------------------------|-----------------------------------------------------------------------------------------------------------------------------------------------------------------|-----------------------------------------------------------------------------------------------------------------|
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| [FASTA](https://en.wikipedia.org/wiki/FASTA_format) | .fas, .fasta, .fa | DNA or protein sequences without annotations | [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 | [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 | [GenomicAnnotations.jl](https://github.com/BioJulia/GenomicAnnotations.jl) |
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| EMBL | .embl | DNA or protein sequences with annotations | [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. | [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. | [XAM.jl](https://github.com/BioJulia/XAM.jl) |
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| [PDB](https://en.wikipedia.org/wiki/Protein_Data_Bank_(file_format)) | .pdb | Protein 3D structure. | [BioStructures.jl](https://github.com/BioJulia/BioStructures.jl), [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 | [BioStructures.jl](https://github.com/BioJulia/BioStructures.jl), [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. | [BioStructures.jl](https://github.com/BioJulia/BioStructures.jl) |
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| [DSSP](https://github.com/PDB-REDO/dssp) | | Protein Secondary Structure | [ProteinSecondaryStructures.jl](https://github.com/BioJulia/ProteinSecondaryStructures.jl) |
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| [STRIDE](https://webclu.bio.wzw.tum.de/stride/) | | Protein Secondary Structure | [ProteinSecondaryStructures.jl](https://github.com/BioJulia/ProteinSecondaryStructures.jl) |
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| [PAF](https://github.com/slimsuite/pafscaff) | .paf | Pairwise mApping Format. | [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 | [MIToS.jl](https://github.com/diegozea/MIToS.jl) |
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| [A3M](https://en.wikipedia.org/wiki/FASTA_format) | .fas | A2M/A3M are a family of FASTA-derived formats used for sequence alignments | [MIToS.jl](https://github.com/diegozea/MIToS.jl) |
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| [PIR](https://www.bioinformatics.nl/tools/crab_pir.html) | .pir | Multiple sequence alignment format | [MIToS.jl](https://github.com/diegozea/MIToS.jl) |
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# Data Structures
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