Questions tagged [sequence-analysis]
Umbrella term for understanding any given nucleic acid sequence code, either as a locus, loci or genome with itself or as a comparison to comparable nucleic acid sequence code either intraspecifically or interspecifically
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I have few genes and would like to retrieve their gene expression. Please any one help me how to retrieve the gene expression
How to retrieve the gene expression for the analyzing up and down regulations? .
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How can I Find DNA sequence of promoter region of a gene?
I have a fungal sequence from Candida albicans, sequenced via Sanger sequencing, that I want to check for quality and contamination.
I have 2 questions:
Could I use Alignment ? or BLAST or ...
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Exploring Amino Acid Patterns in Proteins Through N-gram Analysis [closed]
In our recent research, we delved into the amino acid composition of protein sequences by applying n-gram analysis techniques. By examining the distribution of n-grams ranging from 1-gram to 11-gram, ...
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SARS-CoV-2 sequence used in the AlphaSeq Antibody Datasets to predict binding affinity
Currently we are building a sequence based deep-learning model to predict binding affinity between antibody and antigen. For this we are training a sequence based model with AlphaSeq Antibody dataset (...
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Multi Factor in Deseq2 Gene enrichment analysis
I want to see how the gene expression differs in breast cancer between three species, and I am using DESeqDataSetFromMatrix on my count table.
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How to classify TF motifs by family
I have a FIMO output, the input sequences were putative promoter sequences of several species. I want to graph the positions of these motifs along a horizontal graph, but I want to filter the data by ...
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Recommendations on Motif scoring functions
I am searching for specific transcription factor binding locations on DNA, and ranking them according the their scores.
For this, I am in search of a tool or method that can generate motif scores for ...
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probability of finding a 5 amino acids in a row within a proteome
How to calculate the probability of finding two proteins that share a 5 amino acid long motif from a proteome of around 1067 proteins that have an average length of 65 residues.
The probability of a ...
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Longstitch error make: command: Command not found *** No rule to make target
I installed Longstitch and ran the test script with no issues. The output files matched the expected output files. But when I am now trying to run Longstitch on my own data I am getting this error.
<...
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What does the different sequences represent?
I am using this package nsdpy to download genome sequences from NCBI nucleotide database.
Specifically I am interested in the whole mitochondrial genome of different species, here I will use a subset ...
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Trimmomatic QC report shows drop in the reads and presence of overrepresented sequences
This question was also asked on Biostars
I am performing a de novo genome assembly using Illumina paired-end short reads, sequenced on a NovaSeq X by our collaborator at UCLA.
At present, I am in the ...
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How to find amino acid sequence of a given protein
Is there a way to look up the amino acid sequence of a given protein? For example, what amino acids are used to produce Amylase? I spent hours googling but to no avail. If that's impossible, how can I ...
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paired-end short reads: will one file suffice?
I have a quick question about paired-end short reads. I have multiple genomes that were sequenced with paired-end Illumina NextSeq 200 technology, resulting in two fastq files per sample: ...
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Finding mutations in glycosylation sites
We are going to look at the likely N- and O- glycosylation sites within MUC16 (Q8WXI7 · MUC16_HUMAN)§ by in house long-read DNA sequencing data (PacBio).
Counting the number of tandem repeats is a ...
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stats.sh error in BBmap package
I am trying to calculate the N50 value from the assembled FASTA file. I used stats.sh from the BBmap package. I executed the following command
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