2026-10-14 https://api.researchdata.se/oai-pmh

oai:researchdata.se:doi-10-17044-scilifelab-24039510/0 2023-10-19 subject:ssif:3 subject:ssif:10611 subject:ssif:106 subject:ssif:1 principal:slug:uppsala-university

info:eu-repo/semantics/other http://purl.org/dc/dcmitype/Dataset https://doi.org/10.17044/SCILIFELAB.24039510 3. Comparative population transcriptomics in krill: orthogroups (FASTA, TSV files) https://orcid.org/0000-0002-9081-9663 Medical and Health Sciences Medicin och hälsovetenskap Ecology Ekologi This item contains a gzipped archive with ~13,000 orthogroups used to study molecular evolution in this project. Archive: krill.orthogroups.tar.gz Contents of archive (FILE,SIZE,SPECIES,SAMPLES,SNPs): - krill.proteinortho.tsv - the primary output table from Proteinortho. Describes which protein sequences from which species belong to the same orthogroup. Format according to the standard output of the program. - krill.proteinortho.tsv.seqs.csv - a processed table that also contains the actual sequences line by line (see below). - the alignments directory, which contains all OGs in unaligned and aligned files in FASTA format (see below). Format of the krill.proteinortho.tsv.seqs.csv table The fields are: - NR = orthogroup number - ORTHO_GROUP = orthogroup ID - N_SPECIES = the number of species - N_GENES = the number of genes/sequences in this orthogroup - N_MATCHING[o] = number of sequences matching outgroup species for this orthogroup - N_NON_MATCHING = number of sequences matching ingroup species for this orthogroup - HEADER = the name of this particular sequence - SEQ = the protein sequence Contents of the alignments directory Each orthogroup is represented by up to four FASTA files: - OG*.cds.ginsi.fasta.orig = the original, unaligned and unfiltered sequences - OG*.cds.ginsi.fasta = the aligned and filtered sequences - OG*.cds.ginsi.fasta.without_cold_euphausia.fasta = the aligned and filtered sequences after removing cold-associated Euphausia species - OG*.cds.ginsi.fasta.without_cold_thysanoessa.fasta = the aligned and filtered sequences after removing cold-associated Thysanoessa species https://creativecommons.org/licenses/by-sa/4.0/ Uppsala University Uppsala universitet 2023-10-19T00:00:00Z