dna-sequence Questions
2
Solved
I've got a string:
s = ".,-2gg,,,-2gg,-2gg,,,-2gg,,,,,,,,t,-2gg,,,,,,-2gg,t,,-1gtt,,,,,,,,,-1gt,-3ggg"
and a regular expression I'm using
import re
delre = re.compile('-[0-9]+[ACGTNacgtn...
Gestation asked 20/8, 2024 at 17:18
12
Solved
I have a DNA sequence and would like to get reverse complement of it using Python. It is in one of the columns of a CSV file and I'd like to write the reverse complement to another column in the sa...
Gat asked 7/8, 2014 at 17:50
5
Solved
I have this file:
m64071_220512_054244/12584899/ccs rev pet047-10055 ACGTGCGACCTTGTGA TTGAGGGTTCAAACGTGCGACCTTGTGA
m64071_220512_054244/128321000/ccs rev pet047-10055 ACGTGCGACCTTGTGA TTGAGGGTTCAAA...
Nerta asked 21/12, 2023 at 19:24
3
Solved
I am given a string and have to return False if there is one or more invalid characters, otherwise True. The caveat is that I can only built-in functions and str operations (for example: in, +, ind...
Effortful asked 17/9, 2017 at 18:51
14
Solved
I am working with DNA sequences of length 25 (see examples below). I have a list of 230,000 and need to look for each sequence in the entire genome (toxoplasma gondii parasite). I am not sure how l...
Nador asked 10/3, 2010 at 20:42
5
Solved
I am trying to generate random sequences of DNA in python using random numbers and random strings. But I am getting only one string as my output. For example: If I give DNA of length 5 (String(5)),...
Betthezul asked 18/1, 2014 at 15:6
2
Solved
Background
The Python module regex allows fuzzy matching.
You can specify the allowable number of substitutions (s), insertions (i), deletions (d), and total errors (e).
The fuzzy_counts propert...
Flocculate asked 2/7, 2015 at 20:7
11
Solved
I'm looking for the amount of storage in bytes (MB, GB, TB, etc.) required to store a single human genome. I read a few articles on Wikipedia about DNA, chromosomes, base pairs, genes, and have som...
Drawplate asked 21/1, 2012 at 16:22
5
DNA strings can be of any length comprising any combination of the 5 alphabets (A, T, G, C, N).
What could be the efficient way of compressing DNA string of alphabet comprising 5 alphabets (A, T, G...
Danyluk asked 15/8, 2018 at 13:2
6
Solved
I need to generate a random walk based on the DNA sequence of a virus, given its base pair sequence of 2k base pairs. The sequence looks like "ATGCGTCGTAACGT". The path should turn right for an A, ...
Geodetic asked 10/4, 2011 at 7:1
5
I have this equation for reverse complementing DNA in python:
def complement(s):
basecomplement = {'A': 'T', 'C': 'G', 'G': 'C', 'T': 'A'}
letters = list(s)
letters = [basecomplement[base] f...
Hostetter asked 24/10, 2013 at 15:55
4
Solved
This is a question regarding a more efficient code design:
Assume three aligned DNA sequences (seq1, seq2 and seq3; they are each strings) that represent two genes (gene1 and gene2). Start and sto...
Diphyodont asked 15/1, 2016 at 17:23
3
I am trying to compare two lists to see if there are any matching strings within the lists.
lets say list_1 is
['GAAGGTCGAA', 'GAAGGTCGA', 'AAGGTCGAA', 'GAAGGTCG', 'AAGGTCGA', 'AGGTCGAA', 'GAAG...
Illuviation asked 14/10, 2015 at 0:20
6
Solved
I have searched and was able to find this forum discussion for achieving the effect of overlapping matches.
I also found the following SO question speaking of finding indexes to perform this task,...
Markson asked 12/9, 2014 at 2:56
5
Solved
I have a list of strings (DNA sequence) including A,T,C,G. I want to find all matches and insert into table whose columns are all possible combination of those DNA alphabet (4^k; "k" is length of e...
Firecracker asked 28/10, 2014 at 4:7
4
Solved
Let's say you have a DNA sequence like this :
AATCRVTAA
where R and V are ambiguous values of DNA nucleotides, where R represents either A or G and V represents A, C or G.
Is there a Biopython...
Soundless asked 18/12, 2014 at 17:5
2
Solved
I am a biology graduate student and I taught myself a very limited amount of python in the past few months to deal with some data I have. I am not asking for homework help, this is for a research p...
Karilynn asked 22/10, 2013 at 15:19
1
Solved
Is there an algorithm go generate all possible string combinations of a string (DNA Sequence) by a given number of maximal allowed positions that can variate (maximal Mismatches, maximal Hamming di...
Neese asked 9/10, 2013 at 10:36
3
I am getting a trouble finding an approach to solve this problem.
Input-output sequences are as follows :
**input1 :** aaagctgctagag
**output1 :** a3gct2ag2
**input2 :** aaaaaaagctaagctaag
...
Parachute asked 1/6, 2013 at 9:16
1
Solved
I have tried the mathematica code for making the chaos game for DNA sequences posted in this address:
http://facstaff.unca.edu/mcmcclur/blog/GeneCGR.html
which is like this:
genome = Import["c:\d...
Endymion asked 4/11, 2011 at 12:10
4
Solved
I need to compare the DNA sequences of X and Y chromosomes, and find patterns (composed of around 50-75 base pairs) that are unique to the Y chromosome. Note that these sequence parts can repeat in...
Alessandro asked 27/8, 2010 at 2:43
10
Solved
I'd like to create an rRNA sequence database with a web front end for the lab I work in. It seems common in biology to want to search a large number of sequences using alignment algorithms such as ...
Dempster asked 11/12, 2009 at 19:19
2
Task:
to cluster a large pool of short DNA fragments in classes that share common sub-sequence-patterns and find the consensus sequence of each class.
Pool: ca. 300 sequence fragments
8 - 20 let...
Armhole asked 2/10, 2009 at 12:50
5
Solved
Given these inputs:
my $init_seq = "AAAAAAAAAA" #length 10 bp
my $sub_rate = 0.003;
my $nof_tags = 1000;
my @dna = qw( A C G T );
I want to generate:
One thousand length-10 tags
Substitution...
Fred asked 2/3, 2009 at 9:19
1
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