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11-Aug-2018 New paper describes octave plots for visualizing alpha diversity.

12-Jun-2018 New paper shows that one in five taxonomy annotations in SILVA and Greengenes are wrong.

18-Apr-2018 New paper shows that taxonomy prediction accuracy is <50% for V4 sequences.

05-Oct-2017 PeerJ paper shows low accuracy of closed- and open-ref. QIIME OTUs.

22-Sep-2017 New paper shows 97% threshold is wrong, OTUs should be 99% full-length 16S, 100% for V4.

24-Nov-2016
UPARSE tutorial video posted on YouTube. Make OTUs from MiSeq reads.

 

USEARCH v11

alnout file

The alnout file contains alignments in human-readable format. One alignment is shown for each hit. With local alignments, there may be more than one alignment for a given query-target pair. Below is an example showing a query sequence with one hit to the database.

The -rowlen option sets the length of an alignment row. Default is 60.

For each query sequence, there is a summary report with one line for each hit. In this report, query and target segments are summarized in the format Lo-Hi(Un), giving start-end coordinates (1-based) and number of unaligned letters following the end of the aligned segment. Other information such as percent identity and E-value may also be given, depending on the type of alignment.

Query and target labels and sequence lengths in nucleotides (nt) or amino acids (aa) are given immediately before each alignment.

Summary statistics including number of identities, percent identity, number of gaps etc. are given immediately following each alignment.

Between the query and target sequence is a row of symbols indicating sequence similarity. Identities are given by a vertical bar (|). For protein alignments, these symbols are also used: colon (:) is a match with BLOSUM62 score >= 2.0, period (.) is a positive score < 2.0.

Example

Query >CF1A_DROME
Score     Evalue   %Id  Frame    QueryLo-Hi(Un)   TargetLo-Hi(Un)  Target
343     1e-037   88%     +1        58-279(69)         23-96(44)  POU1_DUGJA

Query 348nt >CF1A_DROME
Target 140aa >POU1_DUGJA

Qry  58 QTDDLEAFAKQFKQRRIKLGFTQADVGLALGTLYGNVFSQTTICRFEALQLSFKNMCKLKPLLQ 249
:         |||| ||| |||||||||:||||||||||||||||||||||||||||||||||||||:||||
Tgt  23 EVDDLEQFAKMFKQRRIKLGYTQADVGLALGTLYGNVFSQTTICRFEALQLSFKNMCKLRPLLQ 86

Qry 250 KWLEEADSTT 279
        ||| ||||..
Tgt  87 KWLHEADSSS 96

Frame +1, 74 cols, 65 ids (88%), 0 gaps (0%), score 343 (137 bits), Evalue 1.1e-037