Reseek documentation

Documentation

Search Searching query structure(s) against a database

Pairwise alignment Structure superposition

Output files Alignments and hit summaries

Structure files File formats for structures and search databases

STRUCTS Specifying structure file(s) on the command line

Converting How to convert between structure file formats

getchains Extract one or more chains from a structure(s) file

Resources Scaling to big database searches

E-values What is an E-value and what threshold should you set?

SCOP40 About SCOP40 benchmark and test results

Figures How to make high-quality protein structure alignment figures

Time, memory and disk space Case study: building and running PDB-95

Prebuilt databases in .bca format including SCOP40, PDB and AFDB

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).