YASS :: genomic similarity search tool

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Data [?]

(1/2) Select the genomic (DNA/RNA) sequence(s) to be compared with YASS (1 sequence self-compared is no main diagonal ⇨ put it twice)

Upload your sequence(s)

choose your file(s), then press select

Paste your sequence(s)

copy/paste your sequence(s), then press select

Use proposed sequence(s)

choose the species/database (hold down [⇧ shift] key + type first letters) and the sequence, then press select


(2/2) Please check the selected DNA sequence(s), then run YASS

Selected DNA sequence(s)
(small fasta/multifasta file with few chunks)
(fasta/multifasta file)

If you use this program, please cite : L. Noe, G. Kucherov, YASS: enhancing the sensitivity of DNA similarity search, 2005, NAR, 33(2)

Parameters (optional) [?]

Scoring system
Scoring matrix (match, transversion, transition, other)
Gap costs (opening, extension) ,
E-value threshold
X-drop threshold
DNA strain (process forward, reverse complement, or both reads of first sequence)
Display quick alignments and statistics [?]
Mask lowercase (do not "index" lowercase letters, they are still used during "extension")
Sort [?]

Advanced parameters (optional) [?]

these options are provided for advanced use of the YASS tool (see the readme file)

Seed parameters
Seed pattern [?] (file)
   new: faster (but with lower sensitivity)
   → select Mow seeds (end of << [autoselect] list)
Hit criterion strategy [?]
Sequence mutation parameters
Indels [?] %
Mutation [?] %
Gapped alignment post-processing
Window range [?] bp, bp
Window incr [?]
(0:disable post-processing)
x factor
Low complexity filter
Entropy (tri-nucl.) [?] bits