Contribute to anvi'o 'omics vocabulary about anvio.org HOT 3 OPEN

+### Indel
+
+Stands for insertion - deletion, of some bases in a DNA sequence. Those are considered short polymorphisms and the differ from point mutations, as the latter are substitutions.
+
+### Protein Structure
+
+Is the three-dimensional arrangement, shaping and folding of atoms in an amino acid-chain molecule (at different levels) to form a functional protein, which can be a monomeric and aggregated into homo- or hetero-polymers.
+
+### Shotgun sequencing
+
+Is the sequencing of the whole nucleotide sequences present in given sample, after being randomly fragmented into short pieces and ligated into known fragments during the sequencing library construction. Its called Shotgun from the concept that a large sequence is essentially broken up in to many, many smaller pieces, similar to how a shotgun shell breaks apart when fired.
+
+### Amplicon Sequencing
+
+(AKA: 16S, ITS, metabarcoding, metataxonomic). Is the sequencing of PCR targeted fragments of interest. It is based on the use of specific primers (degenerated in general) of some marker of interest, commonly resolutive for taxonomic classification (as it should have a variable region flanked by conserved ones).
+
+### Sequence Alignment
+
+Is a technique used to identify (at quantifiable levels) regions of similarity between sequences, which could be nucleotidic (DNA, RNA) or aminoacidic (Proteins). This simmilarities may indicate functional, structural and/or evolutionary relationships between those biological sequences. Aligned sequences are commonly represented as rows within a matrix. Sequence alignments can be used to calculate distances c
+
+### Mapping
+
+Read mapping is the process to align the reads on a reference genomes and/or sequences. Mapper tools takes reference as input and a set of reads to align one by one, allowing some degree of mismatches, indels and clipping of some short fragments on one or the two ends of the reads. This technique maps the positions of reads that are easily recognisable and only occur once in the reference.
+
+### COGs
+
+The database of Clusters of Orthologous Groups of proteins (COGs) is an attempt on phylogenetic classification of the proteins encoded in given set of data to help simplify functional categorization using controlled vocabulary. Each COGs includes proteins that are inferred to be orthologs (direct evolutionary counterparts), maximising their usefulness for functional and evolutionary studies. 
+
+### Annotation
+
+Is the process of identifying functional elements along genome sequences, thus giving meaning to it by by the identification of known elements or by comparison with databases through different analysis, comparison, estimation, precision, and other mining techniques deriving the structural and functional information of a protein or gene. This is a essential step as DNA sequencing generates sequence information without its functional role.