Hi Biostar Group,
I have few sequences which are unclassified fromClostridiaceae 1 family but I want to check whether it belongs to SFB or not.
For this purpose I picked one sequences and classified it in RDP and RDP gave me multiple Hits of SFB
unclassified_Clostridiaceae 1 (16/16/257)
S000008944 not_calculated 0.750 1342 segmented filamentous bacterium; X77814
S000580215 not_calculated 0.747 1263 uncultured bacterium; C23_n17; AY992664
S001416214 not_calculated 0.750 1394 Candidatus Arthromitus sp. SFB-mouse; D86305
S001422660 not_calculated 0.750 1373 uncultured bacterium; MMP7--23; EU791224
S001422681 not_calculated 0.750 1358 uncultured bacterium; MMP7--52; EU791245
S002950053 not_calculated 0.750 1427 Candidatus Arthromitus sp. SFB-mouse-Japan; mouse isolate; AP012202
S002950055 not_calculated 0.750 1427 Candidatus Arthromitus sp. SFB-mouse-Japan; mouse isolate; AP012202
S002950057 not_calculated 0.750 1427 Candidatus Arthromitus sp. SFB-mouse-Japan; mouse isolate; AP012202
S002950059 not_calculated 0.750 1427 Candidatus Arthromitus sp. SFB-mouse-Japan; mouse isolate; AP012202
S002950061 not_calculated 0.750 1427 Candidatus Arthromitus sp. SFB-mouse-Japan; mouse isolate; AP012202
S002950063 not_calculated 0.750 1427 Candidatus Arthromitus sp. SFB-mouse-Japan; mouse isolate; AP012202
S003258921 not_calculated 0.750 1422 Candidatus Arthromitus sp. SFB-mouse-Yit; AP012209
S003258923 not_calculated 0.750 1422 Candidatus Arthromitus sp. SFB-mouse-Yit; AP012209
S003258925 not_calculated 0.750 1422 Candidatus Arthromitus sp. SFB-mouse-Yit; AP012209
S003258927 not_calculated 0.750 1422 Candidatus Arthromitus sp. SFB-mouse-Yit; AP012209
S003258929 not_calculated 0.750 1422 Candidatus Arthromitus sp. SFB-mouse-Yit; AP012209
unclassified_Clostridiales (4/4/8244)
S000580206 not_calculated 0.747 1279 uncultured bacterium; C23_n07; AY992655
S000580265 not_calculated 0.747 1268 uncultured bacterium; C23_p22; AY992714
S000707277 not_calculated 0.750 1360 uncultured bacterium; aab44e08; DQ815666
S000869934 not_calculated 0.753 1256 uncultured bacterium; C14_d09_2; EF614886
But I am not sure whether its a right way to check for SFB in 16sRNA sequences and which particular strain to choose out of all.
I also did blast for same sequence and it gave me Candidatus Arthromitus sp. SFB-mouse-Yit hit with 100% match.
So my question is how to check SFB in 16sRNA sequences specifically.
Looking forward for your reply!!
Note: Each S00 ID has a webpage that can be accessed by appending that ID to the URL: http://rdp.cme.msu.edu/seqmatch/seqmatch_seqrecorddetail.jsp?seqid=. For example, for S000869934, go to http://rdp.cme.msu.edu/seqmatch/seqmatch_seqrecorddetail.jsp?seqid=S000869934
