User: Maria

gravatar for Maria
Maria150
Reputation:
150
Status:
New User
Location:
Last seen:
5 years, 5 months ago
Joined:
7 years, 4 months ago
Email:
a*********@googlemail.com

about me

Posts by Maria

<prev • 31 results • page 1 of 4 • next >
0
votes
0
answers
1.5k
views
0
answers
Multidimensional Dynamic Programming For Global Alignment.
... Is there any formal generalization of the needlman-wunsch algorithm to 3 dimensions instead of pairwise alignment ? I've searched a lot but couldn't find enough details for example I scanned the book "biological sequence alignment " for R. Durbin but I need more details : 1- how to initialize the 3 ...
alignment algorithm msa written 5.5 years ago by Maria150 • updated 5.3 years ago by Biostar ♦♦ 20
2
votes
1
answer
2.8k
views
1
answer
Emboss In Biopython Asequence And Bsequence
... In biopython emboss applications, is it possible that asequence and bsequence attributes of needle/watercommandline object be a variable instead of fasta file ? i.e I want to write the sequence either directly or through variable as shown below bseq= "aaatttccggtt" needle_cline = NeedleCommand ...
python biopython written 5.6 years ago by Maria150 • updated 6 months ago by Biostar ♦♦ 20
0
votes
1
answer
3.1k
views
1
answers
Answer: A: Emboss Needle From Biopython, No Output File
... The Code above give a command that have to be executed manually ...
written 5.6 years ago by Maria150
3
votes
1
answer
3.1k
views
1
answer
Emboss Needle From Biopython, No Output File
... I am trying to use emboss from biopython, I copied into the python commandline the commands from the link above i.e : >>> from Bio.Emboss.Applications import NeedleCommandline >>> needle_cline = NeedleCommandline(asequence="alpha.faa", bsequence="beta.faa", gapopen=10, gapextend ...
windows biopython written 5.6 years ago by Maria150 • updated 2.3 years ago by Biostar ♦♦ 20
1
vote
1
answer
4.1k
views
1
answers
Answer: A: Pairwise2 Biopython Module Get The Score In Variable
... Yes it is possible, for a in pairwise2.align.localms("ACCGT", "ACGC",1,-1,-2,-2): al1,al2, score, begin, end = a ...
written 5.7 years ago by Maria150
1
vote
1
answer
4.1k
views
1
answer
Pairwise2 Biopython Module Get The Score In Variable
... I'm using pairwise2 module from biopython, Is it possible to get the score in a variable and how ? I tried the following and it didn't work : from Bio import pairwise2 from Bio.pairwise2 import format_alignment for a in pairwise2.align.localms("ACCGT", "ACGC",1,-1,-2,-2): score= a.score ...
python alignment biopython written 5.7 years ago by Maria150 • updated 9 months ago by tslakshmipriya900
0
votes
1
answer
2.2k
views
1
answers
Comment: C: Local Alignment Statistical Significance
... 1- But the query sequence could be found in more than one region in the reference sequence, thus I don't only need the alignment with the highest score, I need all the alignment whose length is above some threshhold 3- How to slide the the two sequences ? can you please give a small example ? ...
written 5.7 years ago by Maria150
3
votes
1
answer
2.2k
views
1
answer
Local Alignment Statistical Significance
... I want to align 2 sequences locally (Smith Waterman algorithm) ==> the output will be several alignments some of them unlike others is significant. What I want to do is to test the significance by a randomization/permutation test. And below is my approach: Align S1 to S2 ==> obtain for exa ...
test statistics written 5.7 years ago by Maria150 • updated 4.5 years ago by Biostar ♦♦ 20
1
vote
2
answers
13k
views
2
answers
Comment: C: Ncbi Blast Command Line Align Two Sequences
... The same 2 files when I use as input in the web service I got a result but when I use this command it gives me NO hits found ...
written 5.7 years ago by Maria150
10
votes
2
answers
13k
views
6 follow
2
answers
Ncbi Blast Command Line Align Two Sequences
... I want to align 2 sequences using ncbi blast command line or bioperl script, I am new to blast and I found out that it compare a sequence to a database but what I need it to compare two sequences like in the web service . how to do it ? Thanks in advance ...
blast written 5.7 years ago by Maria150 • updated 5.7 years ago by Ashutosh Pandey11k

Latest awards to Maria

No awards yet. Soon to come :-)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1580 users visited in the last hour