147 votes
Accepted

Why does the SARS-Cov2 coronavirus genome end in aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa (33 a's)?

Good observation! The 3' poly(A) tail is actually a very common feature of positive-strand RNA viruses, including coronaviruses and picornaviruses. For coronaviruses in particular, we know that the ...
  • 1,336
31 votes

Why does the SARS-Cov2 coronavirus genome end in aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa (33 a's)?

This question is quite general, so I'm going to attempt to tie it back to bioinformatics. Background The tree for the current coronavirus is here, showing it is closely related to bat-coronavirus and ...
  • 8,015
20 votes

Why does the SARS-Cov2 coronavirus genome end in aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa (33 a's)?

Some of the other answers here seem quite good; at the same time I think the core answer to the OP's question is maybe a bit hard to tease out of them, so I'd like to try to state it more plainly. It'...
16 votes
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What is 'k' in sequencing?

See IUPAC codes: So, as you can see above, K means "Either G or T".
  • 196
15 votes
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Meaning of BWA-MEM MAPQ scores

First of all, if you want to understand mapping quality (mapQ), ignore RNA-seq mappers. They often produce misleading mapQ because mapQ is not important to RNA-seq anyway. Strictly speaking, you have ...
  • 6,023
15 votes
Accepted

Better aligner than bowtie2?

Bowtie2 is no longer the fastest aligner. Salmon and Kallisto are much faster, but have been designed to optimise RNASeq mapping. Their speed is gained from avoiding a strict base-to-base alignment, ...
  • 12k
13 votes

Why does the SARS-Cov2 coronavirus genome end in aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa (33 a's)?

Not an expert, but some searching on eukaryotic positive-strand RNA viruses seems to show that polyadenylation is not uncommon. For example, Steil, et al., 2010.
  • 561
12 votes
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Definition of "seed" in sequence alignment

The seed is the subset of a read used in the first step of an alignment. Many aligners work by a seed-and-extend model, wherein they first find all regions matching the "seed" and then extend the ...
  • 19.3k
11 votes
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Why does a very strong BLAST hit get lost when I change num_alignments, num_descriptions or max_target_seqs parameter?

I'm trying to figure out why. This will be a longer read, Tl;dr at the end: Doing a match There is a good match of Q against ...
  • 401
11 votes
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BLAST(n): No hits found

There are three possible problems that come to mind. Masking Blast will mask low complexity regions by default. Since your sequence is nothing but Gs, it is a safe bet that it is being masked, so no ...
  • 8,235
11 votes
Accepted

What is a simple command line tool for doing Needleman-Wunsch pair-wise alignment on the command line

You are looking for the needle program from the EMBOSS suite. Available in bioconda. http://emboss.sourceforge.net/apps/...
  • 3,221
11 votes
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A new paper suggests the Corona Virus has "Uncanny similarity of unique inserts in the 2019-nCoV spike protein to HIV-1" - What does this mean?

UPDATE: The article has now been withdrawn with the following note: This paper has been withdrawn by its authors. They intend to revise it in response to comments received from the research ...
  • 3,577
10 votes
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Counting number of possible alignments between two DNA sequences using python

A closed-form solution is offered in An exact formula for the number of alignments between two DNA sequences by Torres, Cabada, and Nieto: $$f(m,n)=\sum_{k=0}^{min(m,n)}2^{k}\binom{m}{k}\binom{n}{k}$$...
9 votes

What is a simple command line tool for doing Needleman-Wunsch pair-wise alignment on the command line

Install biopython with conda and use the following script: ...
  • 19.3k
8 votes
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Why do I get so many insertions from Minimap2 on my Nanopore WGS?

Insertions and deletions are the dominant error mode of long read sequencing, including nanopore sequencing. What you see is not unexpected. Things may have improved by now if you would download the ...
8 votes

How to get fasta alignment file from SAM/BAM file?

I am not sure what you mean by "fasta alignment file". If you mean a multi-sequence alignment (MSA) in the fasta format, you can't get that because SAM keeps pairwise alignments only and doesn't align ...
  • 6,023
7 votes
Accepted

What is local realignment and what is the problem it solves?

SNPs are likely to be created and InDels are likely to be missed. Suppose you have a read, ACTGACTGACTGTAC and you align it to a reference sequence ...
  • 19.3k
7 votes
Accepted

Understanding the initialization of the Needleman-Wunsch algorithm

The first column is added in order to be able to align the sequences. They might be gaps if the alignment ends up beginning in different positions than the first. Without the first empty row and ...
  • 4,622
7 votes

How to create Phylogenetic Trees from fasta files in Python or R?

I would not look for a package for this, but instead build a small pipeline calling external tools with something like the following workflow: Cluster the ~100 sequences with CD-HIT-EST/PSI-CD-HIT or ...
  • 3,577
7 votes

A new paper suggests the Corona Virus has "Uncanny similarity of unique inserts in the 2019-nCoV spike protein to HIV-1" - What does this mean?

Normally "inserts" used in the manuscript are "indels" in protein alignments, short for insertions and deletions. What I think has happened is a group investigating indels in HIV env noticed indels ...
  • 8,015
6 votes

Meaning of BWA-MEM MAPQ scores

Those numbers are not arbitrarily picked (well... maybe 255/60/40 is arbitrarily picked). To convert from log10 Q values like these (also used for error rates in FASTQ files) to probabilities, divide ...
  • 12k
6 votes
Accepted

Does the DNA or RNA of some ethnic groups map better than others' to the human reference genome sequence?

For simple variants like SNPs it would not really be a problem to use the current genome assembly for other ethnic groups. But for more complex variants this could be indeed problematic, however not ...
  • 3,551
6 votes
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Is there a standard definition for "assembly polishing"?

In long-read assembly, "polish" refers to the step to improve the base accuracy of contig sequences. I believe the terminology was originated from the HGAP paper: The final consensus–calling ...
  • 6,023
6 votes
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full visualisation of draft genomes alignment

Found a solution, using D-Genies, worked great. Some examples from their website: Thanks to @user172818.
  • 2,656
6 votes
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Can blat use more than one core/CPU to speed up the alignment?

BLAT can only use one CPU. It is actually not the right tool for full-genome alignment. For "two versions" of the same species, MUMmer and minimap2 are orders of magnitude faster and probably give ...
  • 6,023
6 votes

How to check if indels in VCF files are left or right aligned?

One possibility is to run bcftools norm on the file. At the end it will print out a statistic about how many variants were realigned. I did this for dbSNPv151 (GRCh38) only for chromosome 22 like this:...
  • 1,332
6 votes

Definition of "seed" in sequence alignment

Devon's answer gives a good, concise definition. But it's also helpful to consider why seed-and-extend is used and what benefits it provides. Finding approximate string matches requires operations ...
6 votes
Accepted

Why do ten rows (Figure_1) correspond to 2 bits (Figure_2) in a sequence logo?

Bits are not frequencies. If a position only contains an A (position 3 for example) then you would need 2 questions (bits) to derive that information without a priori knowledge. Is it a G or C? if no ...
6 votes
Accepted

How to understand methylation level?

You are right that a single molecule in a single position is either methylated or not methylated. However: First, assuming your organism of interest is diploid (or of higher ploidy) one of the ...
6 votes

What kind of BLAST do I need to do to accomplish this task?

Clarification Just making sure - you have ~6000 datasets - one for each S.cerevisiae gene of interest - which are made up of homologues of each respective gene? And you want to filter out genes that ...

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