3
votes
Read Clustal file in Python
pyMSAviz may help with this problem.
pyMSAviz is a Python tool with a convenient CLI/API implementation for visualizing MSA files.
For example, you can output MSA figure in PDF format with the ...
- 31
3
votes
Accepted
File format of substitution matrix in clustalw
This example seems to have information on this, looks like it should have this format:
...
- 496
2
votes
Multiple Alignment cost application
I'm not a fan personally, but it is context specific. The problem is that it is heading towards optimisation, particularly algorithmic optimisation. If the alignment is the final calculation - that is ...
M__♦
- 11.9k
2
votes
find conservative regions relative to a specific accession
You can opt for a similarity matrix as output (here is an example). The fact that you would like to judge conservation "relative to a given sequence", you can use this matrix to rank ...
- 3,947
2
votes
ClustalOmega alignment
Have you had a look at your alignment? I personally use Jalview but any alignment viewer should work. Colour > Percentage Identity (or Nucleotide) should help with visualization.
Does the alignment ...
- 881
2
votes
Select representetive sequence within MSA (protein)
I have two suggestions that I used in the past (both using Python/BioPython though). They are arguably the same, but obtained through different paths.
Calculate the (artificial) consensus sequence of ...
- 71
2
votes
multi-sequence alignment of samples with multiple contigs each
in the end, I just loaded the .bam files into artemis and, by inspecting the depth (heat-map), I could check which samples had the genes I was looking for:
- 283
2
votes
multi-sequence alignment of samples with multiple contigs each
If you have a reference genome (or are willing to designate one of your de novo assemblies a reference), you may find QUAST helpful.
QUAST will perform an alignment of all genomes against the ...
- 3,814
2
votes
multi-sequence alignment of samples with multiple contigs each
MUMmer4 is a versatile alignment tool for DNA and protein sequences. It supports one reference genome and up to 32 query genomes. MUMmer4 will align every contig in each genome to the reference genome....
- 387
2
votes
Accepted
Read Clustal file in Python
Ok, figured out a way, not sure its the best one,
nedd to install fpdf2 (pip install fpdf2)
...
- 961
2
votes
Accepted
How to identify sequence origin in DNA shuffle reads?
This is the sort of thing that LAST has been specifically designed to work well for:
LAST is designed for moderately large data (e.g. genomes, DNA reads,
proteomes). It's especially good at finding ...
- 13.8k
2
votes
Read Clustal file in Python
adding, a second answer because the OP request about
I need to import the file and then highlight some specific word
was making me uneasy. I kept using the Pyfpdf2...
- 961
2
votes
Accepted
How do I plot clusters based on DNA sequence alignment?
I think one of the reasons you struggle is that clustering DNA sequences is not a clearly defined task. In general intention of clustering is to reconstruct, or approximate the relatidness of the DNA ...
- 5,517
2
votes
Remove gaps from alignment?
If you want an ungapped alignment, you could do an ungapped alignment (the older read aligners were ungapped, e.g. bowtie). However, I suggest that you don't want an ungapped alignment, you just want ...
- 3,928
2
votes
Remove gaps from alignment?
You may also find useful the BMGE tool (stands for Block Mapping and Gathering with Entropy). BMGE selects regions in a multiple sequence alignment that are suitable for phylogenetic inference by ...
- 56
2
votes
How to create a phylogenetic tree from diverse mitochondrial genomes
It looks like these are random mitochondrial sequences pulled from NCBI, which is probably why the alignments aren't working well.
As a starting point, I recommend you make sure that all the ...
- 13.8k
2
votes
Accepted
How to create a phylogenetic tree from diverse mitochondrial genomes
Your overall approach is cool, given caveats (below) to adapt the method. I can fairly authoritatively say your specific methodological approach will not work regarding its phylogenetic strategy ...
M__♦
- 11.9k
2
votes
Current 'most comprehensive' whole genome alignment resource for human?
The obvious thing missing from your list is the telomere-to-telomere genome assemblies that have been coming out in the last couple years.
Assembly link here.
There are now a few others as well that ...
- 3,814
2
votes
Accepted
BioPython bootstrap is not reliable?
I think this is a bug.
It seems to work if you do this, creating an equivalent Alignment object instead of a MultipleSeqAlignment to give the bootstrap step:
...
- 947
1
vote
How to highlight the specific peptide sequences after performing multiple sequence alignment for the fasta file?
Checkout an MSA visualisation and analysis package that you can load the alignment into. It may not be the newest tool, but I've used Jalview (https://www.jalview.org/) in the past
- 3,928
1
vote
Remove gaps from alignment?
Gblocks is a tool for removing gaps/poorly conserved positions from alignments. Available here. Here is a webserver that runs it for you.
It's a bit old, possibly there are others at this point.
- 3,814
1
vote
drawing multiple sequence alignment as tree in R
Firstly, do check tree is not an empty object, i.e. it uploads the tree file. Secondly, check the path to the alignment is correct ...
M__♦
- 11.9k
1
vote
multi-sequence alignment of samples with multiple contigs each
It won't work on more than 3 genomes at a time, but SynMap3D from the Comparative Genomics webserver (https://genomevolution.org/coge/) should do the trick. I'm mentioning it here because the ...
- 881
1
vote
Generate consensus protein sequence from relatively gappy alignment?
Given the alignment you've presented, there are obvious groups of sequence similarity, but I'm seeing a lot of different peptide sequences in this (e.g. ...
- 13.8k
1
vote
Accepted
Sequence alignment with MUSCLE
HMM Super5 is a hidden Markov model (HMM) where gap penalties and the substitution matrix are the parameters at the centre of the model. That is the answer, thats why you can't change it - it does it ...
M__♦
- 11.9k
1
vote
How to make MSA for contact prediction?
You might have some luck with Parsnp. From the description:
Parsnp was designed to align the core genome of hundreds to thousands of bacterial genomes within a few minutes to few hours. Input can be ...
- 810
1
vote
How to make MSA for contact prediction?
That's a LOT of sequences! I'm doubtful you'd be able to get TripletRes or CCMPred to run at all with an MSA depth of 1.5 million. I suggest pruning your dataset to remove redundant sequences (...
- 11
1
vote
Remove gaps from alignment?
This new tool, CIAlign, talks about some automated removal of gaps in multiple sequence alignments
https://twitter.com/thekatybrown1/status/1306215132670889984
https://github.com/KatyBrown/CIAlign
- 186
1
vote
Multiple Sequence Alignment
It is likely the sequence data in this instance, the more sequences the more chance an issue with the alignment where variations in the gap penalty are observed.
MAFFT outperforms Clustal Omega to ...
M__♦
- 11.9k
1
vote
Multiple Sequence Alignment
The length of the alignment will depend on the model. For example, high gap costs will typically result in shorter alignments, whereas low gap-costs will do the opposite.
Consider the sequences below:
...
- 810
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