6
votes
Accepted
Writing a perl script to holding information for two genes
Perhaps this small test script will help demonstrate some of the principles:
...
- 3,035
5
votes
Range overlap python error with genomic regions
You're reinventing bedtools intersect (or bedops), for which there's already a convenient python module:
...
- 19.2k
3
votes
Calculate the occurrence of motif in sequences (including overlaps) using Python
This is a good task for Biopython:
...
- 3,462
3
votes
Accepted
How to map short sequences to long reads, recovering all multiply-mapped high-quality matches
LAST has given the best results for me when I've tried to do this, although I agree with @user172818 that it's not a good idea to map really short reads. This is due to a combination of natural ...
- 11.7k
3
votes
Range overlap python error with genomic regions
Regarding your python code
If you want the experimental ranges that are entirely contained in one of the reference ranges, you need to have the coordinates in the following order:
...
- 2,960
3
votes
How can I calculate the silent mutation for each position in codon?
Calculate in this context would just mean determine. You don't actually have to change every base to determine whether a change ...
- 19.2k
3
votes
Accepted
Inspection of gene expression in scRNA-seq data
In an ideal world, ribosomal RNA (as seen in your top hit) should be excluded from samples prior to sequencing. Where this is not possible (i.e. in the data that have been presented to you), it would ...
- 11.7k
2
votes
Finding a single open reading frame with ribosomal binding site, using Biopython
From what I can tell, the program output does not indicate whether the open reading frames (ORFs) are preceded by ribosome binding sites (RBSs). I'm not sure what parameters are used when establishing ...
- 121
2
votes
Finding a single open reading frame with ribosomal binding site, using Biopython
You should start by finding all instances of AAGGAGGTG and then look for ORFs that begin 6 to 9 nucleotides downstream of them. By begin, I mean find an AUG codon, ...
- 8,111
2
votes
Writing a perl script to holding information for two genes
The following Perl documentation pages should be informative:
split - for splitting a scalar at all matches of a defined pattern
perlreftut - discusses the approach of anonymous variables and how to ...
- 11.7k
2
votes
Accepted
Find number of possibilities
Let $n$ be the number of rows (in your case $n=5$) and $|O_j|$ the cardinality of $O_i$.
We can calculate the number of compatible columns as sum of the number of $O_i \subseteq O_j$, $O_j \subseteq ...
- 116
2
votes
Accepted
Sequence allignment with suffix array?
What should I do with Ns (ambiguous bases), I've seen some people removing them or replacing them by gaps but this does not seem like the same information? Should they be left in?
As far as I ...
- 758
2
votes
Sequence allignment with suffix array?
Suffix arrays vs Suffix tree is a problem quite often discussed in bioinformatics classes, but it's not that much used in practice. Most of people use already optimized mappers bowtie2 or bwa-mem.
I ...
- 5,287
2
votes
Find species from FASTA files
Are you not allowed to use the web BLAST tool? That's what I use if I need to quickly find out the likely origin of a DNA sequence.
There are command-line ways to do the same thing, but I only use ...
- 11.7k
2
votes
Accepted
How to reconstruct a target string from a large set of overlapping reads
Unless it's not obvious, the problem has no unique solution. An obvious example is a string which uses entirely one character; the problem is then to determine its length, which you can only do ...
- 136
2
votes
I have really skewed RNA-seq data, what's the best way to normalise it? Preferably in R!
I like using DESeq2. There's a great document written by the developers about how to process gene count tables and look at differential expression:
https://bioconductor.org/packages/release/bioc/...
- 11.7k
2
votes
Accepted
How can I draw a diagram of hydrogen bonds only on the basis of C-alpha backbone?
There are three options:
it's a badly phrased Ramachandran plot question
it's a question aimed at the describing the properties of different SS
it's a trick question
φ & ψ can be used to ...
- 3,469
1
vote
Accepted
Generating sequences from HMM
[Comments from other post migrated as answer]
The parenthetical statement in the first bullet point says without corrections. In which case, if an unseen nucleotide has a probability of zero, the ...
- 3,469
1
vote
Which sequencing technologies are considered short read
As mentioned by Greg, list of short-read sequencing platforms is listed on wikipedia.
Of those you mentioned Illumina and Ion Torrent are short-read sequencing platforms.
Usually what makes short ...
1
vote
Construct the Overlap Graph of a Collection of k-mers
You will want to create a self loop for a $k$-mer $s$ whenever $s_1,...,s_{k-1} = s_2,...,s_k$. This will only happen when all of the characters of the $k$-mer are identical, as $s_1=s_2, s_2=s_3,...,...
- 758
1
vote
Generating basic dna sequences in R
Without giving away too much for your homework check out the sample() function in R. Think about how you can pass DNA bases to this function to generate random ...
- 3,071
1
vote
I have really skewed RNA-seq data, what's the best way to normalise it? Preferably in R!
Thanks for all your answers.
Although the pipeline packages would have been useful I was trying to normalise the data before analysing it later and so I used the bestnormalize package which looked ...
- 55
1
vote
I have really skewed RNA-seq data, what's the best way to normalise it? Preferably in R!
Another approach, that does not replace the methods already mentions, but could be useful if you don't have raw counts to start with, or if you want to screen hundreds of genes, and you want to focus ...
- 507
1
vote
how to calculate Pairwise Alignment Scores for blosum62
Your alignment is
SDRVIKAAIFDPIQPDF---G-----PVYFGLGHVH
RDLVERLFILDMI-PGLIKAGDSFPIPVALMINHIF
For each position in the alignment you calculate the score for that ...
- 504
1
vote
Coverage required
According to the book you mentionned Introduction to Genomics SecondEdition by Arthur MLesk p.113
...
1
vote
Function to find ATP binding sites
The problem in your code is that the function atp_binding is not returning any value, but printing it to the stdout.
You should add a return statement with the result you want to save in your output ...
- 111
1
vote
Accepted
Calculate the occurrence of motif in sequences (including overlaps) using Python
I tried to fix the indentation of the code you posted, a typo in some variable names, plus a few other issues that caused it to not work as expected (see the comment in the code):
...
- 2,960
1
vote
Accepted
Finding out proteins that have a similar domain to a specific toxin
A protein domain is a conserved part of a given protein sequence and (tertiary) structure that can evolve, function, and exist independently of the rest of the protein chain.
This is different from ...
- 1,806
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