Sieve analysis is a statistical methodology for identifying evidence of vaccine-induced selective immune pressure on "breakthrough" pathogens in a vaccine efficacy trial. See this review by Edlefsen et al. or these lecture slides from Peter Gilbert for more details. This service can be used to download all the neccesary files for performing a sieve analysis of a vaccine efficacy trial.
A full dataset consists of a treatment assignment file (all patient identifiers are PUB_IDs) and an alignment of all breakthrough genetic sequences and the vaccine immunogen sequence (i.e. the reference).
Treatment CSV file: http://sieve.fredhutch.org/data/treatment.csv?study=VTN502
ptid,treatment
502-0006,placebo
502-0053,placebo
502-0062,vaccine
...
Alignment FASTA file: http://sieve.fredhutch.org/data/alignment.fasta?study=RV144&protein=env&reference=AE
>reference|env|AE
MRVKETQMTWPNLW----KWGTLILGLVIICSASDNLWVTVYYGVPVWRDADTTLFCASD
AKAQETEAHNVWATHACVPTDPNPQELHLENVTENFNMWKNNMVEQMQEDVISLWDQSLK...
>HXB2
MRVKE---KYQHLWRWGWRWGTMLLGMLMICSATEKLWVTVYYGVPVWKEATTTLFCASD
AKAYDTEVHNVWATHACVPTDPNPQEVVLVNVTENFNMWKNDMVEQMHEDIISLWDQSLK...
>AA017
MRVKGTQRNCPNLW----KWGTLILGLVIICSASDNLWVTVYYGVPVWKDAKTTLFCASD
AKAHVPEAHNVWATHACVPTDPNPQEIYLENVTENFNMWKNNMVEQMQEDVISLWDQSLK...
>AA051
MRVKETQMNWPNLW----KWGTLILGLVIICSASDKLWVTVYYGVPVWKDADTTLFCASD
AKAQEPEVHNVWATYACVPTDPNPQELFLENVTENFNMWKNKMAEQMQEDVISLWDQSLK...
E.g. http://sieve.fredhutch.org/data/validanalyses.csv?study=VTN502
protein,reference
gag,MRK
pol,MRK
nef,MRK