Intraspecies sequence-related miRNAs in C. elegans and D. melanogaster were evaluated by manual examination of multiple sequence alignments and 1000 bootstrapped NJ-trees.
Although extensive experimental bench work or human examination of multiple sequence alignments can illuminate such variations, non-automated analysis is tedious and error-prone, especially for long sequences or when more than a few sequences are available.
An examination of multiple sequence alignments (Additional file 3: Figure S1, A-D) indicates amino acid variations at certain highly conserved and structurally relevant positions in TPRs1-4 for choanoflagellates.
After careful examination of multiple-sequence alignment, 114 single nucleotide variations were identified.
Although the lyase domain of members of the LanL and RamC families does not display obvious sequence similarity with that of members of the two other lantipeptide dehydratase families (LanB and LanM), close examination of multiple-sequence alignments exhibits two weakly homologous regions.
Despite its composition of multiple sequences, the two-step examination could be completed within 15 min in-room time, which makes it feasible as a quick test for daily clinical routine.
Sequence logo representation (below) of multiple sequence alignments for C. tritonis with other species (Supplementary Data S8).
A visual examination of the multiple sequence alignments in cluster C and those of the Csl families suggests that most of these non-Csl proteins do not have the characteristic 'D,D,D,QXXRW' motif typically found in Csl/CesA proteins.
Examination of the multiple sequence alignments showed that many unresolved gene trees were due to repeat sequences, also known as low complexity regions (LCRs), in coat proteins.
Here, we performed an examination of multiple categories of QFP sequences in human mtDNA.
The examination of multiple PCR reactions for specific tissues enabled the confirmation of sequence integrity in the database.
