Additional file 1: Table S1. of FRAMA: from RNA-seq data to annotated mRNA assemblies

List of external software. Table S2: NMR transcript data set TCUR, and orthologous transcripts from human, mouse and guinea pig. Multi-species mRNA alignments were constructed independently from those described in the main text, using the sequence database entries as listed. Table S3: Naked mole-rat samples for strand-specific RNA-seq, and produced RNA-seq data. Table S4: Pairwise transcript sequence identities between NMR and related mammals. The analysis is based on 142 multiple sequence alignments of the CDSs of NMR, guinea pig, human and mouse (as listed in Additional file 1: Table S2). Identity values were computed based on gap-masked alignments. Table S5: Statistics of the transcriptome data produced by Trinity (column “transcript assembly”) and subsequently processed using FRAMA (column “transcript catalog”). Table S6: CEGMA results on transcriptome datasets. As defined by CEGMA, ‘complete proteins’ are recovered with >70 % in comparison to CEGMA’s core proteins. ‘Partial proteins’ additionally include proteins, which exceed a certain alignment score threshold. CEGMAs software components were used as suggested: geneid (v1.4), genewise (wise2.2.3-rc7), hmmer (HMMER 3.0), NCBI BLAST+ (2.2.25). Table S7: Source of transcript sequence sets and underlying input data. Table S8: Transcript-genome alignment statistics of curated dataset (TCUR) in hetgla1. The alignments comprise 1473 well-aligned blocks and 81 unaligned or mismatching blocks. Transcripts show 99.9 % average identity within well-aligned blocks. Table S9: Transcript-genome alignment of curated dataset (TCUR) in hetgla2. The alignments comprise 1525 well-aligned blocks and 16 unaligned or mismatching blocks. Transcripts show 99.9 % average identity within well-aligned blocks. Table S10: Correspondence of gene symbols between transcript sets. The evaluation considered gene loci overlapping in the hetgla2 genome sequence, where all transcript-genome alignments of a gene were considered to define the gene locus. Only genes with ascertained function (non-LOC gene symbol) were compared. Table S11: Accession numbers of sequences that are shown in the genome-based transcript map (hetgla2, scaffold JH602043; Fig. 4). Accession numbers for each sequence are listed in the same order as shown in Fig. 4 (from top to bottom). (XLSX 77 kb)