YASS :: genomic similarity search tool

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Options

Here are given some of the most commonly used command line parameters :

The scoring system can be selected by:

You can increase/limit the number of alignments in the result :

Advanced Options


Input

Choose either 1 or 2 nucleic sequences. Note that if only one DNA sequence is selected, then it is compared to itself. YASS input is either (Multi)Fasta or Plain text format :

Fasta file example :

>gi|26245917|ref|NC_004431.1| Escherichia coli CFT073, complete genome
AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGC
TTCTGAACTGGTTACCTGCCGTGAGTAAATTAAAATTTTATTGACTTAGGTCACTAAATACTTTAACCAA
TATAGGCATAGCGCACAGACAGATAAAAATTACAGAGTACACAACA...

Multi-fasta files can be considered as a database (and thus taken as a whole) if given as the second filename parameter. The first file parameter can also be a multi-fasta file, and all the sequences are considered in it (YASS v1.14): use -S to select the one to process.

Output

The option -d 0 shows alignments positions, length and Evalue.

The option -d 1 gives complete alignments in the following format :

*(969588-969895)(124765-125072) Ev: 3.08503e-21 s: 308/308 f
* "MC58" (2272351 bp) / "IX" (439885 bp)
* score = 346 : bitscore = 108.00
* mutations per triplet 29, 71, 34 (1.04e-07) | ts : 64 tv : 70 | entropy : 4.90003

  |969590   |969600   |969610   |969620   |969630   |969640   |969650   |969660 
ACTTATGTTCCTCTGCGCCATATGGGCGAAGGCATGGGCGAGTTCCTGGTTATCGACTCCATTTTGAACGAAGAAGCCGT
|:|||:::.||.||:.||..|.||::::|.|:.|.||..||.|||.:.:||::.:|:|||.:.||:..:||:.|.|.:||
ATTTACACACCGCTAAGCACTCTGAATAATGAAAAGGCAGACTTCACCATTGCAAATTCCTCGTTATCTGAGTACGGTGT
     |124770   |124780   |124790   |124800   |124810   |124820   |124830        

  |969670   |969680   |969690   |969700   |969710   |969720   |969730   |969740 
GATGGCGTTCGAGTACGGCTTTGCCTGCTCCGCACCTGACAAACTGACCATTTGGGAAGCTCAATTCGGTGACTTCGCCA
:||||..|||||:||:||:|.|.|.:...||.|.||.||:.|.||:::|||.|||||:|||||||||||||||||:||.|
AATGGGTTTCGAATATGGTTATTCGCTAACCTCCCCAGATTATCTAGTCATGTGGGAGGCTCAATTCGGTGACTTTGCAA
     |124850   |124860   |124870   |124880   |124890   |124900   |124910        

  |969750   |969760   |969770   |969780   |969790   |969800   |969810   |969820 
ACGGCGCGCAAGTGACTATTGACCAATTCCTGTCTTCAGGCGAAACCAAGTGGGGTCGTTTGTGCGGTCTGACTACCATC
|::..||:||:||.|:||||||||||||:.|..|:...||:|||...||:|||::.|:.:..|.:|||:|:::|.:..::
ATACAGCACAGGTTATTATTGACCAATTTATTGCCGGTGGTGAACAAAAATGGAAGCAACGCTCTGGTTTAGTTTTGTCT
     |124930   |124940   |124950   |124960   |124970   |124980   |124990        

  |969830   |969840   |969850   |969860   |969870   |969880  
CTGCCGCACGGCTACGACGGTCAAGGCCCCGAGCACTCTTCTGCACGCGTAGAACGTTGGTTGCAACT
:|:||.||:||:||:||:||:||:||.||.||:||:||.||||...|..|:|||.|.|..||||||||
TTACCCCATGGTTATGATGGCCAGGGGCCAGAACATTCGTCTGGTAGATTGGAAAGATTCTTGCAACT
     |125010   |125020   |125030   |125040   |125050   |125060 


A script yass2blast.pl is proposed to convert yass -d 1 output in blast full alignment output (or in axt/fasta format):

 Score = 108 bits (346), Expect = 3.08503e-21
 Identities = 174/308 (56%)
 Strand = Plus / Plus


Query: 969588    ACTTATGTTCCTCTGCGCCATATGGGCGAAGGCATGGGCGAGTTCCTGGTTATCGACTCC 969647
                 | |||    || ||  ||  | ||    | |  | ||  || |||    ||    | |||
Sbjct: 124765    ATTTACACACCGCTAAGCACTCTGAATAATGAAAAGGCAGACTTCACCATTGCAAATTCC 124824


Query: 969648    ATTTTGAACGAAGAAGCCGTGATGGCGTTCGAGTACGGCTTTGCCTGCTCCGCACCTGAC 969707
                    ||    ||  | |  || ||||  ||||| || || | | |     || | || || 
Sbjct: 124825    TCGTTATCTGAGTACGGTGTAATGGGTTTCGAATATGGTTATTCGCTAACCTCCCCAGAT 124884


Query: 969708    AAACTGACCATTTGGGAAGCTCAATTCGGTGACTTCGCCAACGGCGCGCAAGTGACTATT 969767
                  | ||   ||| ||||| ||||||||||||||||| || ||    || || || | ||||
Sbjct: 124885    TATCTAGTCATGTGGGAGGCTCAATTCGGTGACTTTGCAAATACAGCACAGGTTATTATT 124944


Query: 969768    GACCAATTCCTGTCTTCAGGCGAAACCAAGTGGGGTCGTTTGTGCGGTCTGACTACCATC 969827
                 ||||||||  |  |    || |||   || |||   |     |  ||| |   |      
Sbjct: 124945    GACCAATTTATTGCCGGTGGTGAACAAAAATGGAAGCAACGCTCTGGTTTAGTTTTGTCT 125004


Query: 969828    CTGCCGCACGGCTACGACGGTCAAGGCCCCGAGCACTCTTCTGCACGCGTAGAACGTTGG 969887
                  | || || || || || || || || || || || || ||||   |  | ||| | |  
Sbjct: 125005    TTACCCCATGGTTATGATGGCCAGGGGCCAGAACATTCGTCTGGTAGATTGGAAAGATTC 125064


Query: 969888    TTGCAACT 969895
                 ||||||||
Sbjct: 125065    TTGCAACT 125072

The option -d 2 produces BLAST tabular output. Can be used to apply BLAST output parsers :

MC58        IX   56.49   308     134     0       969588  969895  124765  125072  3.1e-21 108
MC58        IX   60.84   263     93      10      751895  752157  213618  213880  2.1e-19 102
MC58        IX   59.06   276     100     13      752399  752665  214119  214394  1.9e-15 88.8
MC58        IX   65.52   145     50      0       752066  752210  213789  213933  7e-13   80.2
MC58        IX   58.71   201     83      0       1684840 1685040 423430  423230  4.7e-12 77.5
MC58        IX   58.29   199     77      6       968315  968513  123477  123675  9.4e-09 66.5
MC58        IX   63.72   113     41      0       968988  969100  124159  124271  2.8e-07 61.6
MC58        IX   71.76   85      22      2       773143  773225  370394  370478  2.3e-05 55.2
MC58        IX   71.76   85      22      2       1499839 1499921 370394  370478  2.3e-05 55.2

The option -d 3 produces a very light and easily parsable output :

969588  969895  124765  125072  308     308     f       107.998 3.08503e-21
751895  752157  213618  213880  263     263     f       101.899 2.11464e-19
752399  752665  214119  214394  267     276     f       88.7859 1.87322e-15
752066  752210  213789  213933  145     145     f       80.2473 6.96558e-13
1684840 1685040 423230  423430  201     201     r       77.5028 4.66817e-12
968315  968513  123477  123675  199     199     f       66.5246 9.41687e-09
968988  969100  124159  124271  113     113     f       61.6454 2.77133e-07
773143  773225  370394  370478  83      85      f       55.2415 2.34674e-05
1499839 1499921 370394  370478  83      85      f       55.2415 2.34674e-05
154025  154071  317763  317809  47      47      f       52.8019 0.000127308
968703  968848  123877  124022  146     146     f       52.497  0.000157273

The option -d 4 produces a BED output and the -d 5 produces a PSL output

Advanced parameters