HMM PD0149 - Revision history

Mark: /* How the HMM was built */

2015-10-09T19:56:24Z

‎How the HMM was built

Mark: /* Why built the HMM */

2015-10-09T19:56:15Z

‎Why built the HMM

Mark at 19:55, 9 October 2015

2015-10-09T19:55:59Z

Mark: Created page with "Back to '''List of HMMs''' '''Symbol''': PH_1 '''Name''': PH domain === Why built the HMM === Because our in-house HMM MTMR_GRAM can not detect all PH do..."

2015-10-09T19:55:23Z

Created page with "Back to '''List of HMMs''' '''Symbol''': PH_1 '''Name''': PH domain === Why built the HMM === Because our in-house HMM MTMR_GRAM can not detect all PH do..."

New page

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

'''Symbol''': PH_1

'''Name''': PH domain

=== Why built the HMM ===
Because our in-house HMM [[PD0134|MTMR_GRAM]] can not detect all PH domains in myotubularins, we built the PH domain from [http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=cd13223 CDD profile].

=== How the HMM was built ===
We downloaded the alignment from CDD, edited the align to get the regions used by CDD to build the profile, built HMM by hmmbuild, and validated by protein phosphatases of the nine genomes.

Using domain E-value threshold 0.1 for both [[PD0134|MTMR_GRAM]] and PD0149 (PH_1) HMMs, among 76 myotubularins in 9 genomes, 58 have PH domains, PD0149 (PH_1) found 2 that were missed by [[PD0134|MTMR_GRAM]]; and [[PD0134|MTMR_GRAM]] found 25 that were missed by PD0149 (PH_1).

← Older revision		Revision as of 19:56, 9 October 2015
Line 11:		Line 11:
	We downloaded the alignment from CDD, edited the align to get the regions used by CDD to build the profile, built HMM by hmmbuild, and validated by protein phosphatases of the nine genomes.		We downloaded the alignment from CDD, edited the align to get the regions used by CDD to build the profile, built HMM by hmmbuild, and validated by protein phosphatases of the nine genomes.

−	Using domain E-value threshold 0.1 for both [[HMM_PD0134\|MTMR_GRAM]] and PD0149 (PH_1) HMMs, among 76 myotubularins in 9 genomes, 58 have PH domains, PD0149 (PH_1) found 2 that were missed by [[HMM_PD0134\|MTMR_GRAM]]; and [[~~PD0134~~\|MTMR_GRAM]] found 25 that were missed by PD0149 (PH_1).	+	Using domain E-value threshold 0.1 for both [[HMM_PD0134\|MTMR_GRAM]] and PD0149 (PH_1) HMMs, among 76 myotubularins in 9 genomes, 58 have PH domains, PD0149 (PH_1) found 2 that were missed by [[HMM_PD0134\|MTMR_GRAM]]; and [[HMM_PD0134\|MTMR_GRAM]] found 25 that were missed by PD0149 (PH_1).

← Older revision		Revision as of 19:55, 9 October 2015
Line 11:		Line 11:
	We downloaded the alignment from CDD, edited the align to get the regions used by CDD to build the profile, built HMM by hmmbuild, and validated by protein phosphatases of the nine genomes.		We downloaded the alignment from CDD, edited the align to get the regions used by CDD to build the profile, built HMM by hmmbuild, and validated by protein phosphatases of the nine genomes.

−	Using domain E-value threshold 0.1 for both [[~~PD0134~~\|MTMR_GRAM]] and PD0149 (PH_1) HMMs, among 76 myotubularins in 9 genomes, 58 have PH domains, PD0149 (PH_1) found 2 that were missed by [[~~PD0134~~\|MTMR_GRAM]]; and [[PD0134\|MTMR_GRAM]] found 25 that were missed by PD0149 (PH_1).	+	Using domain E-value threshold 0.1 for both [[HMM_PD0134\|MTMR_GRAM]] and PD0149 (PH_1) HMMs, among 76 myotubularins in 9 genomes, 58 have PH domains, PD0149 (PH_1) found 2 that were missed by [[HMM_PD0134\|MTMR_GRAM]]; and [[PD0134\|MTMR_GRAM]] found 25 that were missed by PD0149 (PH_1).

@@ Line 6: / Line 6: @@
 === Why built the HMM ===
-Because our in-house HMM [[PD0134|MTMR_GRAM]] can not detect all PH domains in myotubularins, we built the PH domain from [http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=cd13223 CDD profile].
+Because our in-house HMM [[HMM_PD0134|MTMR_GRAM]] can not detect all PH domains in myotubularins, we built the PH domain from [http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=cd13223 CDD profile].
 === How the HMM was built ===