Reseek documentation

C-alpha file format
Reseek supports a new format called C-alpha, files must have .cal extension.

This is a text format which represents the C-alpha atoms for one or more structure chains as seen in the following example:

>1ABC
S       26.877  49.597  36.595
E       23.362  50.107  35.318
F       23.745  46.560  33.839
D       24.931  44.797  36.962
Y       22.888  42.289  38.824    
... etc ...

Each chain starts with a > in column one followed by a label, as in FASTA format. Following the label, there is one line for each amino acid. There are four tab-separated fields: the one-letter amino acid code followed by X, Y and Z coordinates of the C-alpha atom.

C-alpha format is typically 30x to 60x smaller than PDB or mmCIF format.

Use the convert command to create a C-alpha file, for example:

reseek -convert mystructsdir/ -cal mystructs.cal

Video talks on 16S data analysis posted.

URMAP ultra-fast read mapper posted (paper).

~20% of taxonomy annotations in SILVA and Greengenes are wrong (paper).

Taxonomy prediction is <50% accurate for 16S V4 sequences (paper).

97% OTU threshold is wrong for species, should be 99% for full-length 16S, 100% V4 (paper).