PMC

(a) Growth of the database file size(Bytes) while incorporating more RNA-seq data. (b) Increase in the percentage of covered splice junctions compared to RefSeq. (c) Increase in the number of splice junctions expressed in splice graph database which does not exist in RefSeq.

(a) Given RNA-seq read, find overlapping regions with the existing splice graph. (b) Split and add nodes. (r₁, node s₁ is split into nodes u₁ and u₂, and node u₃ is added.) (c) Assign edges for each spliced-read. (d) Revisit each pair of contiguous nodes. The nodes are merged if there is no edge at the boundaries. (Nodes u₁ and u₂ are merged, while e₅ is added between u₂ and u₃.)

(a) By traversing the graph using a depth first search(DFS), we generate a sequence from the first visited start to end node path. (b) While traversing in DFS, when we encounter an outgoing edge that is already visited, only maintain a length L −1 suffix. (c) While traversing in DFS, when we encounter an incoming edge that is already visited, only maintain a length L−1 prefix. (d) For a pair of sequences(paths) with a prefix-suffix match, combine two sequences.

(a) Shows a novel gene area where two peptides are identified in a non-genomic region. (b) Two peptides with alternative splice junctions. Peptide T.LNVNGQE:IVYSMENEK.L is supported by 13 split mapped RNA-seq reads, and R.EIKK:QHTSFQVSGPKEEIVYSMENEK.L is supported by 40 reads. (c) Peptide ‘TIVFTVPLSQCQMVSPMISK.E’ matches in a different frame compared to the gene eef-2. Two neighboring peptides, ‘R.FIEPIEDIPSGNIAGLVGVDQYL:S.R’, and ‘G.HVFEESQVTGTPMFVV:R.L’ are identified with 1 bp deletion, that allow for the frame-shift to occur.