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Bioinformatics : Recent Questions and Answers (Page 17)

Find answers to your questions about Bioinformatics or help others by answering their Bioinformatics questions.

Blastp MSA to the same length

To generate aligned protein sequence truncate to the same length, I use blastp in biopython for MSA. I have multiple queries and one subject sequence. However, the alignment never returns...

Asked on 07/14/2021

0 answer

ATAC-seq macs2 peak splitting in sliding windows

This question has also been asked on Biostars I used macs2 to call peaks for atac-seq data. now my goal is to split the peaks into 50...

Asked on 07/12/2021 by user5191

1 answer

Get dataframe from an LipidomicsExperiment when using lipidr package

With the library lipidr lipidomics data has been normalized using the function normalize_pqn(), and I need to get the normalized data to perform further statistical analysis without using lipidr library,...

Asked on 07/11/2021

0 answer

Comparing the genetic similarity of human genome and mice/monkey genome - where can I find a list of genes?

I am trying to start a side project where I verify the claim that human and mice/monkey share 99% of their genes. I hope to learn the basics of doing...

Asked on 07/10/2021 by i_dont_know

1 answer

Subset FASTA file by species name

I have a problem: I've managed to download a massive fasta file of 1500 sequences, but now I want to split them into separate fasta files based on the genus....

Asked on 07/10/2021 by tahunami

2 answer

Querying metadata (GDC) using a filter

I have been trying to access the GDC metadata with python through the filter below. However, this code I have been using always yields a blank tsv file. Any help...

Asked on 07/10/2021 by lab

1 answer

Get gene sequence based on the annotation

I've got the reference genome with Python like so:sequences_by_chr = {}with gzip.open("data/Zea_mays.B73_RefGen_v4.dna.toplevel.fa.gz", "rt") as f: for seq in SeqIO.parse(f, "fasta"): ...

Asked on 07/09/2021 by Igor Filippov

3 answer

Hg38 annotation tracks retrieval

I want to retrieve an annotation object (as GRanges) containing different UCSC annotation tracks such as CpG Islands, TSS, TFBS and promoters for hg38 Human reference genome. But "UCSC Genes"...

Asked on 07/06/2021 by TRakesh

1 answer

Installation of PRANK MSA in WLS Ubuntu 20.04 LTS

I want to install PRANK on the Windows 10 Linux subsystem (Ubuntu 20.04 LTS), I have followed the installation instructions to no avail.wget http://wasabiapp.org/download/prank/prank.source.140603.tgztar xvzf prank.source.140603.tgzcd...

Asked on 07/05/2021

1 answer

Transcription factor targets for Human and Mouse genes

I want to get transcription factor targets for my list of genes (For Human and Mouse) I have found ENCODE Transcription Factor Targets database (The link is given below). But...

Asked on 07/05/2021

2 answer

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