tag:blogger.com,1999:blog-1315445647083902393.post6879369949055421315..comments2024-03-25T18:48:55.048+05:30Comments on BioGem Blog: Hydrophobicity Plot using BioPythonProf. Dr. T. Ashok Kumarhttp://www.blogger.com/profile/14677658375016995194noreply@blogger.comBlogger7125tag:blogger.com,1999:blog-1315445647083902393.post-5154034884378275142019-03-23T10:04:27.689+05:302019-03-23T10:04:27.689+05:30Dear Rohit Jain,
This program is to generate hydro...Dear Rohit Jain,<br />This program is to generate hydrophobicity plot using dataset (Hydrophic values of 20 amino acids. Kyte-Doolittle scale values are used in this program) from the amino acid sequence. The basic concept is plotting 2D graph through x and y coordinate numbers.<br />Generating a plot using the alignment gap is meaningless. It will break the graph plot.Prof. Dr. T. Ashok Kumarhttps://www.blogger.com/profile/14677658375016995194noreply@blogger.comtag:blogger.com,1999:blog-1315445647083902393.post-56485715538134078732019-03-21T23:49:47.527+05:302019-03-21T23:49:47.527+05:30Looking forward to your reply.Looking forward to your reply.Anonymoushttps://www.blogger.com/profile/02493411581100017963noreply@blogger.comtag:blogger.com,1999:blog-1315445647083902393.post-32183938568524037012019-03-21T23:49:29.553+05:302019-03-21T23:49:29.553+05:30My name is Rohit JainMy name is Rohit JainAnonymoushttps://www.blogger.com/profile/02493411581100017963noreply@blogger.comtag:blogger.com,1999:blog-1315445647083902393.post-21704276269149719052019-03-21T23:49:11.181+05:302019-03-21T23:49:11.181+05:30Hello Ashok. I will like to calculate hydrophobici...Hello Ashok. I will like to calculate hydrophobicity on aligned sequences. I have aligned sequences in FASTA format. There are gaps in aligned sequences. I need output as values for every sequence which i can then avaerage. Can it be done ?<br />Thanks. Anonymoushttps://www.blogger.com/profile/02493411581100017963noreply@blogger.comtag:blogger.com,1999:blog-1315445647083902393.post-26355319190464848912017-09-19T15:23:23.188+05:302017-09-19T15:23:23.188+05:30Thank you very much.Thank you very much.Anonymoushttps://www.blogger.com/profile/14780399167902176029noreply@blogger.comtag:blogger.com,1999:blog-1315445647083902393.post-58829498608670479862017-09-12T19:36:34.706+05:302017-09-12T19:36:34.706+05:30{ 'Ala': 1.290, 'Arg': 0.960, '...{ 'Ala': 1.290, 'Arg': 0.960, 'Asn': 0.900, 'Asp': 1.040, 'Cys': 1.110, 'Gln': 1.270, 'Glu': 1.440, 'Gly': 0.560, 'His': 1.220, 'Ile': 0.970, 'Leu': 1.300, 'Lys': 1.230, 'Met': 1.470, 'Phe': 1.070, 'Pro': 0.520, 'Ser': 0.820, 'Thr': 0.820, 'Trp': 0.990, 'Tyr': 0.720, 'Val': 0.910 }<br /><br />Reference: http://web.expasy.org/protscale/pscale/alpha-helixLevitt.htmlProf. Dr. T. Ashok Kumarhttps://www.blogger.com/profile/14677658375016995194noreply@blogger.comtag:blogger.com,1999:blog-1315445647083902393.post-68377188698571052992017-09-12T18:18:06.554+05:302017-09-12T18:18:06.554+05:30Thank you for your posts. They are really helpful....Thank you for your posts. They are really helpful.<br /><br />I have a question: to calculate hydrophobicity of the entire TM helix, do we have to take mean value of all residues?Anonymoushttps://www.blogger.com/profile/14780399167902176029noreply@blogger.com