Help!
I am looking for a software (such as Ssrtool or Tandem Repeats Finder) to help me spot motifs in my multiple (thousands) proteins,...
23 results in 0.0047 seconds.
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Question: Finding repeats in proteins
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A way to calculate mean divergence for lots of sequences?
Hi,
So I have some sequences of repetitive elements (~13k à 120bp) and am wondering if there is a good way to calculate the (mean) divergence... -
SOLiD for Genomes
Does SOLiD work well for genomes with a lot of repeats? Theoretically it should, but in practice?
Thanks, -
What's happening about my kmer spectrum? Heterozygous or repeats?
I am doing a denovo genome sequencing and i get the kmer spectrum using clean reads of two paired end libarary data(see attach files). From the plot,... -
To mask or not to mask?
Hi all,
I read several threads here and in other bio-forums about masking genome regions. There are different opinions, from don't mask... -
Using BBMap to determine possible repeat scaffolds/contigs
Hello,
I used BBmap to find the coverage of a draft genome I have with this command:...Code:bbmap.sh in1=reads1.fq in2=reads2.fq ref=scaffolds.fasta
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RepeatMasker v4.0.5 no output created
I am running RepeatMasker v4.0.5
the command line is :
RepeatMasker -lib my_own_lib.fasta -dir output_directory output_name... -
DFam database: what on earth is a "cut and paste" repeat?
Hi All,
Downloaded some repeat-masking data from DFam (http://www.dfam.org/) and along with LINE, SINE, LTR etc repeats it includes a... -
Single Nucleotide Repeat Help Needed
I am trying to find the "true" genotype of several loci from target capture data. These are single nucleotide repeats between 15-18 bps long.... -
High Error Rate After Repeat In Reads
I have obtained whole genome sequencing data for human patients. I notice that after a repeat region, the rest of the read is typically soft-clipped.... -
Reverse complementary reads in Mummmer
The repeat-match program in mummer, claims to return reverse complementary repeats, and mark them with 'r'. However, I found that the repeats returned... -
how to summarize information for a gene from bam file
I have very basic question about bam files, it may be very obvious but kind of stacked.
I would like to see how many LINE,SINE etc are... -
Statistical treatment of biological reps from pooled samples
Hi, I have a theoretical question. I know that it's important to do biological reps when doing differential expression RNA-seq experiments (3 seems to... -
repeats
I am trying to find a repeat regions (not Transposons). Is there a way i can find a 50 bp region repeating across the genome ?. Need to find the number... -
MiSeq paired-end sequencing of an amplicon with 45bp inverted repeat
Hi,
I have a plasmid library that looks like this:
uniq-seq1___45bp__sequence-of-interest___45bp__uniq-seq2
The ...
