Skip to main content

Questions tagged [genome]

for questions related to whole genome analyses. For questions related to individual genes, use tag gene instead. Questions specific to format (like fasta) should be tagged with a format-specific tag.

32 questions with no upvoted or accepted answers
Filter by
Sorted by
Tagged with
5 votes
1 answer
2k views

How to install DnaSP on a Mac

I need to install DnaSp, a nice GUI originally written for Windows for the population genetics of nucleotide sequence data. However, its not working on my mac. I'm using wine to install it using these ...
Mollie Passacantando's user avatar
4 votes
0 answers
36 views

Do RepeatModeler results contain functional domains?

The repeat families predicted by RepeatModeler contain known transposable elements (TEs) and unknown ones. How do we know whether some of these may actually: within a functional domain of a gene or ...
Life_Searching_Steps's user avatar
3 votes
0 answers
23 views

What is the reason for the discrepancy between the total number of non-N bases and the total length of the human genome assembly on the NCBI website?

I've been digging into the human genome assembly data and I've stumbled upon a discrepancy that I couldn't resolve on my own. I'd appreciate any insights or explanations from the biology community. ...
CuriousPotato's user avatar
2 votes
1 answer
19 views

GBS- 'Failure' in, Per base sequence content, Sequence Duplication Levels, and Adapter Content

I have a GBS sequence on the Illumina platform that in the FASTQC quality report has “Failure” in : Per tile sequence quality, Per base sequence content, Sequence Duplication Levels and Adapter ...
Gabriela Carvalho da Silva's user avatar
2 votes
0 answers
51 views

Running Genome Scale Metabolic Model but with different concentration of medium composition

I want to run a simulation with COBRApy for my bacterial Genome Scale Metabolic Model (GEM). I want it to run on different concentration of medium composition such as 0% NaCl, 10% NaCl, and 20% NaCl. ...
raysteven's user avatar
2 votes
0 answers
53 views

Is there a way antiSMASH can be used to screen a large number of genomes just for one type of biosynthetic gene cluster?

When we use antismash command with the genome sequence file as follows: antismash GCA_002095535.1_ASM209553v1_genomic.gbff it screens the genome for all the ...
snap_v's user avatar
  • 21
2 votes
1 answer
76 views

Is there a way to extract spike sequence from a Sars-CoV-2 complete genome (preferably in Python)?

I have a complete genome sequence of a Sars-CoV-2 variant, but I am only interested in the Spike sequence? I should note that I am not a biologist (nor bioinformatics). The complete genome looks like ...
mac179's user avatar
  • 121
2 votes
0 answers
11 views

Flux balance Analysis, Result interpretation, solver Solver Heuristics

i am new to modelling of cellular networks, and I have two basic questions, regarding the result interpration. I am using the COBRAToolbox to do a flux balance analysis of a whole genome scale model ...
Martin Welte's user avatar
2 votes
0 answers
32 views

What Cellbase resources are 0-indexed, and which are 1-indexed?

The UCSC Genome Browser Team is clear about that the genome browser GUI indexing which is 1-based, closed interval. Genomic sequence retrieval via the UCSC REST API is 1-based, closed interval. All ...
mRotten's user avatar
  • 192
1 vote
0 answers
36 views

How should I prepare human genome reference file?

Currently I'm trying to perform whole mtDNA sequencing and mapping to reference genome to extract variants. To minimise the nuMT (nuclear mt DNA segment), I'm going to use the hg19 human genome as a ...
uri's user avatar
  • 85
1 vote
0 answers
135 views

bwa mem hangs after a few thousand reads

I am trying to align a bunch of paired sample fastq files using bwa mem. My original command was: ...
padakpatek's user avatar
1 vote
0 answers
43 views

How to use HGTECTOR tool for identifying HGT genes in a bacterial genome?

I wanted to know the HGT genes in a Metabacillus strain and I noticed that several papers use HGTector for this purpose. I installed HGTector through conda and tried to download the database for ...
K_081's user avatar
  • 149
1 vote
0 answers
55 views

What is the current state-of-the-art for classifying the ancestry groups of VCF files?

I'm wondering which tool or program is: Most updated; doesn't use a superseded algorithm Runs very quickly (ideally, under 30s per VCF file) Able to be automated in some way for a large number of ...
BigMistake's user avatar
1 vote
1 answer
103 views

Lower case vs. upper case nucleotids in sequence vs. dots at the end

What is the difference between lower case and upper case nucleotides in a sequence? My other question is what are the dots at the end of the sequence? Some examples are shown below: GGgG,GGgG,GGgG,...
David Khutsishvili's user avatar
1 vote
0 answers
42 views

System specifications for NGS data analysis

I have a 3.7 GB whole genome data of a eukaryote, for which genome assembly, gene prediction, and annotation steps have to be performed. In some time I would also need to analyze the transcriptome ...
Shakunthala's user avatar
1 vote
0 answers
26 views

Why does gene count increase drastically after scaffolding with Hi-C data?

I have a conceptual question. I have a diploid, outcrossing plant genome assembly of ~1.1 Gb size. The original assembly is generated from PacBio reads. After genome annotation with the ...
Anik Dutta's user avatar
1 vote
1 answer
751 views

tensorflow nn_model for DNA sequences: Matrix size-incompatible: In[0]: [2,1], In[1]: [784,300]

Hope anyone can help a beginner here. I'm building a proof-of concept tensorflow classifier for DNA sequences. However, the NN model does not let through train and test vectors saying the matrix size ...
monade's user avatar
  • 11
1 vote
0 answers
137 views

How to extract certain genes including non-coding regions?

I would like to look at the non-coding regions of some genes. I have around 1000 full genome assemblies and I was able to extract the nucleotide sequences for certain proteins with ...
Soerendip's user avatar
  • 1,295
1 vote
0 answers
15 views

How do I include repeat purity, default slippage, default stutter, and minimum flanking (left and right) in Tandem Repeat Finder's output?

I am attempting to create a markerInfoFile for use in a program called popSTR (GitHub Documentation: https://github.com/DecodeGenetics/popSTR). The marker info file should contain information about ...
annabelperry's user avatar
1 vote
0 answers
35 views

Is it possible to determine the genomic context of a gene in a Whole Genome Shotgun project?

I performed several BLAST searches and identified several genes of interest in a Whole Genome Shotgun (wgs) project. I know that gene X is located on scaffold 1234, from nucleotide 1 - 2250, while ...
Leah's user avatar
  • 123
1 vote
0 answers
21 views

Finding gene name from human genome using SP1 transcrition factor binding site from Postion Weight Matrix

I have a list binding site motif of SP1 transcription factor which collects from PWMScan tools. Actually this tool scan whole human genome and give the entire binding motif list. From that list of ...
nayan de's user avatar
1 vote
0 answers
181 views

Can Mauve export indels or is there an whole-genome aligner that can export indels?

I have aligned two whole genomes of the same species in Mauve using progressiveMauve. One of the genomes is 2 megabases longer than the other so I know it must contain some insertions. Looking at the ...
Biomagician's user avatar
  • 2,459
0 votes
0 answers
47 views

How do you download metadata for TCGA pathology slides

I downloaded the TCGA pathology slides for the SKCM project and the files are all a name such as "TCGA-3N-A9WB-01Z-00-DX1.A9950ED4-9480-455C-AE0D-8E076D4DA432.svs". How do you get the ...
DeepLearner123's user avatar
0 votes
0 answers
35 views

Error while opening xmfa generated by progressiveMauve

I used commandline progressiveMauve to align two genome .gbk files. The alignment was successful. But when I try to visualize the final .xmfa file with Mauve, I get the following error. ...
venkatesh war's user avatar
0 votes
0 answers
23 views

Gene Expression Database for Psychological Disorders

Is there a comprehensive database available online of gene expression across the brain taken from individuals with psychological conditions? Resources like the Allen Institute's Human Brain Map (link ...
Lambda's user avatar
  • 101
0 votes
0 answers
89 views

Help me to calculate Heaps Alpha value from the roary pangenome pipeline result?

I need to know whether my pan-genome is open or closed. For that, I need to calculate the ...
Kumar's user avatar
  • 109
0 votes
0 answers
211 views

How to manually curate a genome assembly for sequence variation or error?

I have a PacBio HiFi assembly of 1.1 Gb from a heterozygous species. I have aligned this assembly against a reference genome which is around 0.9 Gb. I can see that there are quite a few INDELs, ...
Anik Dutta's user avatar
0 votes
0 answers
32 views

Search for specific sequence in group of bacterial genomes

I have a group of L. plantarum genomes. I identified the pangenome using Roary. From the pangenome, I was able to identify unique 'genes' for some of the strains. One of these (actually several were, ...
Mark's user avatar
  • 143
0 votes
0 answers
244 views

How to filter a genome assembly consistsing of a large number of contigs?

I did some de novo genome assemblies with Illumina PE data using SPAdes, whereas most of them consisting of a large number of contigs(>1000). I have several questions below. Do we need to filter ...
YP CHEN's user avatar
  • 81
0 votes
0 answers
47 views

Coding vs non-coding DNA length

I am trying to calculate the total exonic length (in bp) in order to see where the coding-noncoding ratio of roughly 1% to 99% comes from. We know all chromosomes total about 3 billion base pairs. So ...
janeu's user avatar
  • 1
-1 votes
1 answer
35 views

Where can you download functional domain labels of the human genome?

I'm visualizing where mutations occur in a gene, and would like to add functional domains to the plots. I have some trouble locating sources to download data on functional domains. The dataset should ...
Sofie's user avatar
  • 1
-1 votes
1 answer
35 views

Evolutionary speaking, what are the constraints on having new mutations?

Evolutionary speaking, some mutations lead to better fitness of an organism and its adaptation to the environment changes, but I was wondering if there are some constraints on having new mutations. ...
Negin's user avatar
  • 107