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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: ...
Alex Reynolds's user avatar
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: ...
Devon Ryan's user avatar
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3 votes

Calculate the occurrence of motif in sequences (including overlaps) using Python

This is a good task for Biopython: ...
Chris_Rands's user avatar
  • 3,958
3 votes
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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 ...
gringer's user avatar
  • 14.7k
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: ...
bli's user avatar
  • 3,130
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 ...
Devon Ryan's user avatar
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3 votes
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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 ...
gringer's user avatar
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3 votes

Is there any function in Biopython to convert a DNA sequence from ambiguous to unambiguous?

from Bio.Seq import Seq coding_dna = Seq("AAYGANAGYCARAGYAAR") print(coding_dna.translate()) This gives NXSQSK So .translate() will read a degenerate ...
M__'s user avatar
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3 votes

Is there any function in Biopython to convert a DNA sequence from ambiguous to unambiguous?

M__'s approach is good, but, as explained, some subset of the unambiguous DNA sequences will not be recovered because of the ambiguity in reverse-translation due to the degeneracy of the genetic code. ...
acvill's user avatar
  • 613
3 votes

1.What size PCR product will be generated using the primers (bold and underlined) in the sequence below?

Without giving too much of the "what they want you to do yourself" bits of this away, here are a few explanations of the image that may help you answer this question: As mentioned in the ...
gringer's user avatar
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3 votes

Help Understanding the Greedy Motif Search Algorithm from Textbook

I have been similarly stuck on the Bioinformatics textbook motif problems in Rosalind, mostly because the documentation included with the problems is sparse, useless, or nonexistent. The mouseover for ...
gringer's user avatar
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3 votes
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Help Understanding the Greedy Motif Search Algorithm from Textbook

I figured this out after rereading the chapter a few times. I am going to try my best to describe the solution here for anyone else who runs into this issue, since I don't think this was meant to be ...
David Rouleau's user avatar
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 ...
Ghoti's user avatar
  • 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, ...
terdon's user avatar
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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 ...
gringer's user avatar
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2 votes
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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 ...
Bluescreen's user avatar
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/...
gringer's user avatar
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2 votes
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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 ...
Throckmorton's user avatar
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 ...
Kamil S Jaron's user avatar
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 ...
gringer's user avatar
  • 14.7k
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 ...
Pseudonym's user avatar
  • 136
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 ...
Matteo Ferla's user avatar
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2 votes
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DESeq2 and EdgeR

I think your question has been answered very well here: https://www.biostars.org/p/284775/ If you want to go deeper perhaps you can look at this paper by Li et al. https://genomebiology.biomedcentral....
Avamys's user avatar
  • 118
2 votes
Accepted

probability of finding a 5 amino acids in a row within a proteome

Its just significant at 2% 0.055 . 65 . 1067 = 0.021 (its actually 0.02 - see note) Where critical probability is 0.05, i.e. 5% There are 20 aa so 1/20 probability of random occurrence. The ...
M__'s user avatar
  • 12.8k
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,...,...
Throckmorton's user avatar
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 ...
conchoecia's user avatar
  • 3,181
1 vote

BioPython - Retrieve sequence records from pubmed database

Answer from @devon-ryan, converted from comment: They meant the nucleotide database.

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