Visual inspection process. Matches in the alignments are colored in blue and mismatches in red. Amino acids aligned to gaps are indicated in green. Panels (A) to (D) illustrate alignments of two protein sequences classified as isoforms (panels (A) and (B)) or as paralogs (panels (C) and (D)). The sequences shown in panel (A) feature a shared subsequence (a putative constitutive exon), marked in blue. The upper sequence features an additional exon at the beginning (marked in green) that is missing in the lower sequence. In contrast, a putative exon at the end (also shown in green) is found in the lower sequence only. Comparison of the two putative isoforms shown in panel (B) reveals two constitutive exons in the middle and towards the end of the alignment, colored in blue (the only mismatch is interpreted as a sequencing error, or a polymorphism). These are separated by a stretch of amino acids aligned to gaps, interpreted as an exon skipped in the lower sequence. At the beginning of the alignment, the upper sequence features a long stretch of amino acids aligned to gaps and a few mismatches; two mutually exclusive exons are a plausible interpretation, since the lower sequence (starting with G and not with M) is incomplete and its first exon is probably much longer. At the end of the alignment both sequences feature a stretch of mismatches and gaps (colored in red), interpreted as mutually exclusive exons (indicated by a black frame). The sequences compared in panel (C) give rise to a sample of the paralog class. In general, the alignment features many mismatches, interpreted as substitutions, and six stretches of amino acids aligned to gaps (putative deletions). Panel (D) illustrates another putative paralog. Besides a shared stretch (featuring numerous substitutions) in the middle of the alignment, the upper sequence features putative deletions, or missing exons. It may thus be a case of an isoform of a paralog.