In brief, an alignment graph is composed of vertices corresponding to non-overlapping genomic regions with edges indicating matches between regions.
Colors were used to visually encode base conservation and to indicate matching, non-matching and similar nucleotides [ 76, 77].
When tissue samples from SARS victims were scanned, the slides indicated matches with coronaviruses not only from humans, but also ones that normally infect turkeys and cows -- suggesting a strain that has never been seen before.
Solid lines indicate matching pairs with low costs while dotted lines indicate costly matching pairs.
Stars indicate matches to goldfish olfactory epithelium.
In the transcription, + indicates matched transcript in EST database, – indicates no matched transcript in EST database.
miRNAs in italics indicate matches with one GU wobble.
The MS/MS spectrum in the bottom panel indicates matches of predominant fragment ions to the peptide sequence.
The solid lines and dot in miRNA: mRNA alignments indicate matched RNA base pairs and GU mismatch, respectively.
The Dot plot figure was generated using MUMmer version 3.22 [ 47] and indicates matching sequences, with codirectional and reversed regions of synteny shown in red and blue, respectively.
