How to anlyse CD-HIT2d-Result_to filter non-homologous

Question

[Nitha]

Hi All,

I have compared 2 whole protein (human with bacteria), cd-hit2d program was performed with 0.7 (70%), I have got some result. I'm not able to analyse the result. I have to check the result and take non-homologous sequence..can anyone help me to find it..

Thanks

[Ram]

You're going to have to elaborate on "Im not able to analyse". CD HIT is a clustering tool. Unless outliers were filtered, or there were homologous outliers, you will find them in singleton clusters. Start with the singletons and work your way upwards to maybe 2- or 3-sized clusters.

[Nitha]

Thanks Ram, for replying!

I have got the out put db2.cluster sorted and I have to take the Accession number id, to retrieve the sequence. taking id manually from the result for big data its takes time.. If I am not wrong, i have to take each id of from matched number then followed novel one..How to take this accession number separately..wtr there is any method or program.. plz guide me

>Cluster 2
0    5256nt, >CAX10866... *
1    5256nt, >CAX10866... at +/100.00%
>Cluster 3
0    4596nt, >CAX11273... *
1    4596nt, >CAX11273... at +/100.00%
>Cluster 4
0    4350nt, >CAX10594... *
1    4350nt, >CAX10594... at +/100.00%

0    5256nt, >CAX10867... *

0    5256nt, >CAX10898... *