# Tag Info

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

### 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

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

This is a good task for Biopython: ...
• 3,462
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

### 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

### 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
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

### 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

### 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

### 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
Accepted

• 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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