aLbAc
  • Member for 5 years, 10 months
  • Last seen more than a month ago
  • Edinburgh, United Kingdom
Bioinformatics basics
2 votes

Genbank is a database of nucleotide sequences that are public. NCBI stands for "National Center for Biotechnology Information" (in the US). Entrez is NCBI's retrieval system. You can find more ...

View answer
Publicly available resources for learning metagenomics
1 votes

In the paper here compared lots of different tools for the different parts of the anlysis in metagenomics. It is a comprehensive study in which several labs participated. You need to take into ...

View answer
Estimation of the amount of bacteria
Accepted answer
1 votes

This is a very standard method. The idea is that you have a culture of bacteria on an agar plate. During the incubation each bacteria forms a colony. After a few hours of growing the colonies grow and ...

View answer
Common Metrics of Assessing DNA Sequence Quality
Accepted answer
1 votes

As mention in the comments Phred scores are the quality scores for most sequencing platforms. This value expresses the probability of a base is being called wrongly. You can find more information here....

View answer
Obtaining a mapping of RefSeq ACs to Uniprot ACs
Accepted answer
1 votes

You have a bunch of options: You can use Biomart. Biomart is a standalone tool, but also have a pyton and R libraries. So it gives you more options depending on your preferred programming language. ...

View answer
How to reduce the number of sequences in a Multiple Sequence Alignment?
0 votes

The bioconductor package "ShortRead" might be what you are after. It has a function "clean" to remove sequences with ambiguous bases. It also can remove duplicates if you need to.

View answer
What is the best way to find which domains in a list of InterPro IDs are catalytic?
0 votes

In InterPro you can do a search "by text" and type in "catalytic". It gives you a list of IDs with description and you can download the list.

View answer
Methods for microbial identification in soil
0 votes

16S is still one of the most poplular methods of idenifying organisms. The technique is very well stablish and it works well. However, it has some limitations, for example there is a significant ...

View answer
How to determine which is the nucleotide sequence of a gene?
Accepted answer
0 votes

You run a blast of your sequence. Then explore the results and you'll see somewhere that says "strand" and is indication whether is plus/minus. https://blast.ncbi.nlm.nih.gov/Blast.cgi Also blast ...

View answer
How do I look for pathogen in water with a microscope? Is it possible?
Accepted answer
0 votes

Yes your teacher is right. In a microscope you can see microorganisms. Now the question is to identify them as pathogens. I guess what your teacher has in mind is to use specific culture mediums for ...

View answer
Do all multiple sequence alignments employ global alignment algorithms?
0 votes

Multiple sequence alignment is a very complex task and there are several approaches depending on what you are looking for. A global alignment might find the overall closest region. However, it is a ...

View answer