Mark at 17:53, 9 October 2015

2015-10-09T17:53:57Z

Mark: Created page with "Back to '''List of HMMs''' '''Symbol''': SAC9_NTD1 '''Name''': SAC9, N-Terminal Domain 1 === Why built the HMM? === We noticed Ddis051 ..."

2015-10-09T05:49:43Z

Created page with "Back to '''List of HMMs''' '''Symbol''': SAC9_NTD1 '''Name''': SAC9, N-Terminal Domain 1 === Why built the HMM? === We noticed Ddis051 ..."

New page

Back to '''[[HMM|List of HMMs]]'''

'''Symbol''': SAC9_NTD1

'''Name''': SAC9, N-Terminal Domain 1

=== Why built the HMM? ===
We noticed [[Phosphatase_Gene_Ddis051|Ddis051]] has a tail not similar to other SACs in the nine genomes.

=== How the HMM is built ===
We then PSI-BLASTed the tail (from the C-terminal of Sac_PD to the C-terminal of the full sequence) against Swiss-Prot. Because there were very few hits, we then PSI-BLASTed the same region against Ref-Seq. We downloaded the sequences, removed redundant sequences (at threshold 70% identity), aligned the sequences and manually adjusted the alignments. We found there were actually two conserved regions, which we named SAC_NTD1 and [[HMM_PD0146|SAC_NTD2]], respectively. We built two HMMs for each of the two regions.

@@ Line 1: / Line 1: @@
 Back to '''[[HMM|List of HMMs]]'''
-'''Symbol''': SAC9_NTD1
+'''Symbol''': SAC9_CTD1
-'''Name''': SAC9, N-Terminal Domain 1
+'''Name''': SAC9, C-Terminal Domain 1
 === Why built the HMM? ===
@@ Line 9: / Line 9: @@
 === How the HMM is built ===
-We then PSI-BLASTed the tail (from the C-terminal of Sac_PD to the C-terminal of the full sequence) against Swiss-Prot. Because there were very few hits, we then PSI-BLASTed the same region against Ref-Seq. We downloaded the sequences, removed redundant sequences (at threshold 70% identity), aligned the sequences and manually adjusted the alignments. We found there were actually two conserved regions, which we named SAC_NTD1 and [[HMM_PD0146|SAC_NTD2]], respectively. We built two HMMs for each of the two regions.
+We then PSI-BLASTed the tail (from the C-terminal of Sac_PD to the C-terminal of the full sequence) against Swiss-Prot. Because there were very few hits, we then PSI-BLASTed the same region against Ref-Seq. We downloaded the sequences, removed redundant sequences (at threshold 70% identity), aligned the sequences and manually adjusted the alignments. We found there were actually two conserved regions, which we named SAC_CTD1 and [[HMM_PD0146|SAC_CTD2]], respectively. We built two HMMs for each of the two regions.

HMM PD0145 - Revision history

Mark at 17:53, 9 October 2015

Mark: Created page with "Back to '''List of HMMs''' '''Symbol''': SAC9_NTD1 '''Name''': SAC9, N-Terminal Domain 1 === Why built the HMM? === We noticed Ddis051 ..."