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  • sivasubramani
    Member
    • Apr 2011
    • 13
    #1

    cd-hit output clarification

    Hi all,

    I got an output from cd-hit-est as follows.
    >Cluster 1
    0 1997nt, >Locus_3753_Transcript_3/6_Confidence_0.182_Length_1997_UP10_UP11... at 208:1784:3900:5486/+/92.67%
    1 15188nt, >Locus_416_Transcript_101/105_Confidence_0.255_Length_15188_UP1... at 11777:1:4159:15952/-/85.81%
    2 15605nt, >Locus_2273_Transcript_25/30_Confidence_0.598_Length_15605_UP7... at 3700:15605:4159:16064/+/100.00%
    3 16064nt, >Locus_2273_Transcript_26/30_Confidence_0.576_Length_16064_UP7... *
    4 15812nt, >Locus_2273_Transcript_30/30_Confidence_0.598_Length_15812_UP7... at 1844:15812:2097:16064/+/99.90%
    5 1973nt, >Locus_1056_Transcript_4/7_Confidence_0.185_Length_1973_UP4... at 340:1760:4052:5486/+/93.33%
    6 15398nt, >Locus_2370_Transcript_21/28_Confidence_0.628_Length_15398_UP2... at 2321:14533:2883:15100/+/99.27%

    In the above what does the tailing information tell us.. For eg: at 2321:14533:2883:15100/+/99.27%.

    What individual number means,

    Thanks,
    Tags: None
  • Kennels
    Senior Member
    • Feb 2011
    • 149
    #2
    Originally posted by sivasubramani View Post
    Hi all,

    I got an output from cd-hit-est as follows.
    >Cluster 1
    0 1997nt, >Locus_3753_Transcript_3/6_Confidence_0.182_Length_1997_UP10_UP11... at 208:1784:3900:5486/+/92.67%
    1 15188nt, >Locus_416_Transcript_101/105_Confidence_0.255_Length_15188_UP1... at 11777:1:4159:15952/-/85.81%
    2 15605nt, >Locus_2273_Transcript_25/30_Confidence_0.598_Length_15605_UP7... at 3700:15605:4159:16064/+/100.00%
    3 16064nt, >Locus_2273_Transcript_26/30_Confidence_0.576_Length_16064_UP7... *
    4 15812nt, >Locus_2273_Transcript_30/30_Confidence_0.598_Length_15812_UP7... at 1844:15812:2097:16064/+/99.90%
    5 1973nt, >Locus_1056_Transcript_4/7_Confidence_0.185_Length_1973_UP4... at 340:1760:4052:5486/+/93.33%
    6 15398nt, >Locus_2370_Transcript_21/28_Confidence_0.628_Length_15398_UP2... at 2321:14533:2883:15100/+/99.27%

    In the above what does the tailing information tell us.. For eg: at 2321:14533:2883:15100/+/99.27%.

    What individual number means,

    Thanks,
    It is the alignment coordinates of the subsequence, representative sequence, strand, and identity.

    For example, your representative sequence from this cluster would be sequence 3, denoted by the asterisk.

    3 16064nt, >Locus_2273_Transcript_26/30_Confidence_0.576_Length_16064_UP7... *

    So for sequence 4, the subsequence aligned from pos 1844-15812, to pos 2097-16064 of the representative sequence, on the plus strand, at 99.9% identity.

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