note - FIZ Karlsruhe
note - FIZ Karlsruhe
note - FIZ Karlsruhe
You also want an ePaper? Increase the reach of your titles
YUMPU automatically turns print PDFs into web optimized ePapers that Google loves.
Introduction to similarity searching<br />
Similarity Searching and FSORT<br />
DGENE answer sets may be grouped by underlying source publications using Family SORT<br />
(FSORT). FSORT gathers multiple sequence hits together via publication, application, and/or<br />
priority numbers. FSORT organizes answers into two subsets: multiple sequence hit (multi-record)<br />
families and single sequence hit (individual-record) families. When FSORT is used on an answer<br />
set previously sorted by SCORE, the two FSORT subsets each separately retain their SCORE sort<br />
order. FSORT makes it possible to review, e.g. just the most similar sequence answer for each<br />
family group, or all the sequence hits from a single family group.<br />
Recall the Search Question (page 20)…<br />
Page 40 | GENESEQ on STN (DGENE) Workshop Manual<br />
Find patent sequences with similarity to the Banana Bunchy Top Virus<br />
(BBTV) Replication Initiation Protein (NCBI: AAG44003):<br />
MSSFKWCFTLNYSSAAEREDFLALLKEEELNYAVVGDEVAPSSGQKHLQG<br />
YLSLKKSIKLGGLKKKYSSRAHWERARGSDEDNAKYCSKETLILELGFPA<br />
SQGSNRRKLSEMVSRSPERMRIEQPEIYHRYTSVKKLKKFKEEFVHPCLD<br />
RPWQIQLTEAIDEEPDDRSIIWVYGPNGNEGKSTYAKSLMKKDWFYTRGG<br />
KKENILFSYVDEGSEKHIVFDIPRCNQDYLNYDVIEALKDRVIESTKYKP<br />
IKLVELINIHVIVMANFMPEFCKISEDRIKIIYC<br />
Search Strategy<br />
To conduct a BLAST similarity search, and display answers sorted<br />
by patent family…<br />
Step 1 Upload the sequence and conduct a BLAST search<br />
Step 2 Sort the answers by descending similarity score<br />
Step 3 Sort by patent family with FSORT<br />
Step 4 Display selected answers using DISPLAY PFAM
Change language