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.
27
questions with no upvoted or accepted answers
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What does it mean if aligned genomes are not of the same length?
I am aligning 4 genomes of Psuedomonas chlororaphis using progressive mauve software. Command used:
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5
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1
answer
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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 ...
4
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1
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51
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How to promote assemblies into genomes in NCBI?
Note: I've never submitted an assembly/genome to NCBI, so excuse if my perspective is flawed.
I'm working with Drosophila subobscura. (spring fruit fly)
I see here https://www.ncbi.nlm.nih.gov/data-...
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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
...
3
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2
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54
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Do additional peaks in percent GC of PacBio gDNA reads indicate contamination?
I have two sets of PacBio reads from genomic DNA of an Aspergillus species that were made from separate preps of the culture. One of them has two additional peaks at 38% and 60% in the percent GC ...
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2
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2
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Where do I get a large reference VCF?
I would like to download a large .vcf file containing many (hundreds or thousands) of samples. Ideally, I would download different population-specific .vcf files, but the ability to sort/filter by ...
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2
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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 ...
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2
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1
answer
54
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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 ...
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2
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0
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11
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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 ...
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2
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31
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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 ...
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What tools can I use to look up my alleles, genotypes, or phenotypes from my sequenced DNA (WGS)?
(I am not a Bioinformatics expert, please forgive and educate me if I've used any wrong terms or assumptions here)
I bought a "Whole Genome Sequence" kit, which gave me the following VCF ...
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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 ...
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1
vote
1
answer
51
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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,...
1
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36
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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 ...
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1
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0
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21
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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 ...
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1
vote
1
answer
500
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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 ...
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1
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0
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107
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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 ...
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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 ...
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1
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0
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35
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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 ...
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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 ...
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168
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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 ...
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57
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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 ...
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90
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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, ...
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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, ...
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173
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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 ...
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44
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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 ...
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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. ...
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