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: ...
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: ...
user avatar
  • 19.2k
3 votes

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

This is a good task for Biopython: ...
user avatar
  • 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 ...
user avatar
  • 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: ...
user avatar
  • 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 ...
user avatar
  • 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 ...
user avatar
  • 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 ...
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, ...
user avatar
  • 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 ...
user avatar
  • 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 ...
user avatar
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 ...
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 ...
user avatar
  • 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 ...
user avatar
  • 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 ...
user avatar
  • 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/...
user avatar
  • 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 ...
user avatar
  • 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 ...
user avatar
  • 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,...,...
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 ...
user avatar
  • 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 ...
user avatar
  • 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 ...
user avatar
  • 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 ...
user avatar
  • 504
1 vote

Coverage required

According to the book you mentionned Introduction to Genomics SecondEdition by Arthur MLesk p.113 ...
user avatar
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 ...
user avatar
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): ...
user avatar
  • 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 ...
user avatar
  • 1,806

Only top scored, non community-wiki answers of a minimum length are eligible