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Questions tagged [dna]

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2 votes
1 answer
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Is there a database of oligonucleotide duplex sequences and their melting temperatures

I am looking for melting temperatures of oligonucleotide duplexes, but I am having trouble finding data. Can be DNA-DNA, DNA-RNA, or RNA-RNA duplexes, native or modified nucleotides.
biologist774's user avatar
1 vote
2 answers
35 views

How to download the same 18S rRNA gene region for multiple species?

I need 18S rRNA gene sequences for a wide variety of eukaryotic species. I know that Ensembl has this gene sequence, but I don't understand what is the correct protocol to download the sequences. I ...
Mirk's user avatar
  • 33
2 votes
1 answer
38 views

How many ML tree should I build?

I created a phylogenetic tree of 328 species using RAxML. I run the ML algorithm 20 times and I chose the best tree (the one with the highest likelihood). The choice of 20 iterations was based on a ...
Mirko's user avatar
  • 267
2 votes
2 answers
73 views

Sequence Alignment for sequences with the same length

I am doing research on a new method of optimizing sequence alignment process (Needleman - Wunsch algorithm) but the idea would only work with sequences that have the same length. I am wondering if ...
MirzaK's user avatar
  • 21
3 votes
1 answer
169 views

1.What size PCR product will be generated using the primers (bold and underlined) in the sequence below?

I would like to know the steps of this question and how to determine the forward and the reverse primers and also the length of the sequence, without using NCBI. If you could explain and give an ...
Teo's user avatar
  • 31
0 votes
0 answers
31 views

Is there a method/web server to generate Position-specific scoring matrix (PSSM) for nucleotide sequences (DNA/RNA)?

Just like, PSI-BLAST is avaialble to generate a PSSM matrix for peptides, is there a web server where we can generate PSSM for DNA/RNA? I want to find homologous sequences to a given RNA sequence.
majumderS's user avatar
1 vote
1 answer
67 views

What options are there for visualising DNA sequences?

I typically see several ways of visualising DNA sequences and I would like to know when (best) to use them? For example, I sometimes see the letter codes GATC, sometimes I see colours, sometimes I see ...
Scott McKenzie's user avatar
2 votes
3 answers
36 views

detecting DNA of possible infection on cell line

we've done Whole Genome Sequencing with Illumina on DNA extracted from cell lines, where some are suspected to have been infected by something (viral, bacterial, not sure). I've tried running ...
719016's user avatar
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1 vote
1 answer
34 views

Seeking Guidance on Designing DNA Sequences with Specific Criteria

Dear Bioinformatics Community, I hope you're all doing well. I am currently working on a project that requires designing some 10 nucleotide single-stranded DNAs, (preferably), with specific criteria. ...
Hashem's user avatar
  • 11