User: fareehakanwal90

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New User
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Pakistan
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4 months, 3 weeks ago
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5 years, 1 month ago
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Posts by fareehakanwal90

<prev • 19 results • page 1 of 2 • next >
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nucleotide relative solvent accessibility
... Hi, I am trying to characterize DNA nucleotides from PDB files into buried and accessible regions based on their accessible surface area. For definitions, i need relative accessibility. I am using NACCESS and I do get relative accessibilities for the protein residues but for the DNA, it is alway ...
nucleotides naccess dna written 4 months ago by fareehakanwal9020
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hydrogen bonds in a pdb file through gromacs
... Can I use gromacs to calculate hydrogen bonds within a single pdb file? I do not have a tpr file. ...
gromacs written 13 months ago by fareehakanwal9020
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protein-dna homology models
... Hi, Can anyone guide me on how do I make a homology model of protein-dna complex using modeller? thanks ...
protein-dna homology model modeller written 17 months ago by fareehakanwal9020
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Pairwise Alignment; sequence identity and query coverage
... hello everyone, I want to calculate query coverage and sequence identity of my nucleotide alignment through python. can anyone tell me how to do that? P.S I dont want to do it through blast. I have the alignments, just need a code that can calculate sequence identity and query coverage. ...
rna-seq written 4.9 years ago by fareehakanwal9020
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Comment: C: Biopython ; pdb file parsing
... no its generated by a tool. here it is: ATOM  A16HY  P     C 12724     -52.726 -98.396 -23.094  1.00 83.28           P ATOM  A16HZ  OP1   C 12724     -53.551 -97.182 -22.818  1.00 79.93           O ATOM  A16I0  OP2   C 12724     -52.137 -98.580 -24.459  1.00 69.10           O ATOM  A16I1  O5'   C 1 ...
written 4.9 years ago by fareehakanwal9020
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Comment: C: Biopython ; pdb file parsing
... here is my code: from Bio.PDB import * from itertools import groupby from operator import itemgetter parser=PDBParser() structure=parser.get_structure('X', '4wwt_loop_mcannotate.pdb') faa=open('4wwt_loop_mcannotate.pd','w') #fasta=[] reslist=[] structure=parser.get_structure('X' , '4wwt_loop_mcanno ...
written 4.9 years ago by fareehakanwal9020
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Biopython ; pdb file parsing
... How do I extract a specific residue from a pdb file though biopython? for example I have to extract 23,24th and 27th residue only. How do i do that? ...
rna-seq written 4.9 years ago by fareehakanwal9020
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Pairwise Alignment, Biopython : Bio.pairwise2
... hello, I am trying to do pairwise alignment of sequences in my data set. I am currently using Bio.pairwise2 module for this. My data set however, is saved in the files. Is there a way to pass files containing sequences to the paiwise2 as input argument? I know the longer way of reading it and then ...
biopython written 4.9 years ago by fareehakanwal9020 • updated 4.9 years ago by Peter5.8k
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Comment: C: Pairwise2 Biopython Module Get The Score In Variable
... is it possible to give the sequence files as input to pairwise2?? ...
written 4.9 years ago by fareehakanwal9020
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Comment: C: Biopython Protparam
... were you able to solve it? I am also facing the same problem now   ...
written 4.9 years ago by fareehakanwal9020

Latest awards to fareehakanwal90

Popular Question 2.5 years ago, created a question with more than 1,000 views. For Pairwise Alignment; sequence identity and query coverage
Popular Question 2.5 years ago, created a question with more than 1,000 views. For Biopython ; pdb file parsing
Popular Question 2.5 years ago, created a question with more than 1,000 views. For interpretation of RNA secondary structure
Popular Question 3.4 years ago, created a question with more than 1,000 views. For interpretation of RNA secondary structure
Popular Question 3.4 years ago, created a question with more than 1,000 views. For utilities in vienna-rna package

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