Histidines, arginines or prolines are preferred immediately prior to, and after, aggregating sequences in the proteome.
The sequence variation of the irregular mtDNA could be read from all the observed variable sites by filtering those sites that were present in the aggregate sequence of the single cells (table S1).
In several cases, the determination of a cell (lysate from certain well in a 96-well plate) yielded a sequence different from the aggregate sequence of single cells from the same sample by many homoplasmic mutations, and the sequence variation of this mtDNA type was directly read from the determined sequence.
To prevent server overloading, aggregate sequence lengths up to 100,000 bases are allowed (equal to 100 sequences with an average length of 1000 nucleotides).
Nevertheless CP8 exhibits significant sequence identity with CP220, ranging from 56% up to 100% over a total aggregate sequence length of 11470 bp.
Here, we provide a complete protocol optimized for large aggregate sequence intervals and demonstrate its utility with the capture of all predicted amino acid coding sequence from 3,038 human genes using 241,700 60-mer oligonucleotides.
The maximum match is a combination of the following two factors: (1) the size of the common graph determined by mapping and (2) the aggregate sequence similarity between nodes mapped to one another.
Interestingly, although most SH2 domains did not harbour aggregating βC sequences, the large majority still had histidine, arginine or proline flanking the βC sequence on each side (see alignment in [ 2]).
Aggregating peptide sequences are common within the hydrophobic core of globular proteins [ 23].
Practically, we count the occurrence of all k possible k-mers in the raw metagenomics sequence dataset (palindromic k-mers are aggregated when sequencing direction is arbitrary) and evaluate their distribution using a metric based on the information theory of Shannon [ 22].
