Pat, I’m testing out the 600bp chem again. Illumina insists they’ve fixed the issues. I’ll let you know how that looks in the next few weeks.
Juanjo-I’m with Pat. attaching a name isn’t worth much, esp if the named sequence is distant from your sequence. Embrace that the world of sediment microbiology is largely unknown!
Can you see why similarity isn’t being calculated? I don’t think s_ab score should be interpreted as equal to similarity.
3. A similarity score. SeqMatch reports the percent sequence identity over all pairwise comparable positions when run with aligned myRDP sequences. (Comparable positions are aligned positions containing a base in both sequences). Note that the rank order may differ between S_ab and pairwise identity scores, but the top 20 S_ab scores will contain the closest sequence by pairwise identity about 95% of the time (Cole et al). If two sequences do not overlap, the similarity between these two sequences will be displayed as “?”.
4. A seqmatch score (S_ab). These are the number of (unique) 7-base oligomers shared between your sequence and a given RDP sequence divided by the lowest number of unique oligos in either of the two sequences.