All Questions
Tagged with phylogenetics multiple-sequence-alignment
23 questions
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16
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How can I include the start and end sequence number while doing MSA alignment with any alignment tool like CLUSTALW?
I have this assignment to align sequences from the domains of 5 different proteins. I extracted the domain sequences. I have done the alignment, but I realize I need to number each sequence (since ...
- 23
2
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0
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45
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How to create a dataset of contact maps of homologous proteins?
Disclaimer: I am a machine learning researcher working on network science and want to use proteins to test an algorithm of mine using real-world data. My bioinformatics knowledge is minimal.
I need to ...
- 121
1
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2
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74
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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 ...
- 33
1
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1
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189
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All against all sequence alignment
I have a large set of protein sequences and would like to create a "similarity matrix" out of them (for phylo trees later). So I have to run n(n-1) ...
- 195
3
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2
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107
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What is the best way to acquire protein isoform sequence alignment?
[Update] Thanks @terdon. To clarify my question:
I have a bunch of protein isoforms sequences (produced by the transcripts in the figure) and I want to align protein products (e.g., proteins produced ...
- 31
0
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1
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142
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Aligning sequences with multiple genetic codes!
I am doing a project on duplicated genes and I have a major difficulty on how to align sequences that use different genetic codes. I work with fasta files that contain sequences of protein coding ...
- 59
4
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2
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196
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BioPython bootstrap is not reliable?
Here i will show you a minimal working example of code and as you can see the support values for the tree is always 100.
I am using synthetic sequences of 100bp for 6 elements. The sequences have been ...
- 317
4
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2
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276
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How to create a phylogenetic tree from diverse mitochondrial genomes
I would like to create a phylogenetic tree for the most species in my dataset.
I'm starting with around 1200 species, but since it's not good practice to align short and long sequences I tried ...
- 317
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65
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SNP How to detect regions of erratic pairwise alignment?
I have clusters of DNA sequences that contain some mutations. All the sequences in a cluster should contain the same mutations.
As the mutations aren't known, those clusters of sequences were pairwise-...
- 181
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1
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174
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Mapping List of Probes/Primers/Short Oligos to a Reference Fasta/q
Could you help me bioinformatics SE people.
So I have been duckduckgo-ing up a storm and even consulted the AI overlords and haven't come up with a solid way to do this, but it is so fundamental to ...
- 51
3
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3
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299
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Read Clustal file in Python
This question was also asked on StackOverflow
I have a multiple sequence alignment (MSA) file derived from mafft in clustal format which I want to import into Python and save into a PDF file. I need ...
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98
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How to identify sequence origin in DNA shuffle reads?
The data
I have a large number of reads from sequences that were generated by randomly shuffling regions of two parent sequences together. See the following image:
The regions that are shuffled are ...
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2
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1
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200
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drawing multiple sequence alignment as tree in R
I am very new here. Please help me with my codes as am trying to draw multiple sequence alignment as tree suing ggtree package in R and i have following error.
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- 31
6
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4
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2k
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multi-sequence alignment of samples with multiple contigs each
I want to perform a multi-sequence alignment on 12 samples that clustered based on cgMLST. Ultimate goal is to find out whether they differ by the presence of a few genes.
I have performed multi-...
- 283
1
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2
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102
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Generate consensus protein sequence from relatively gappy alignment?
I would like to know what would be the best way to generate a full-length consensus sequence?
I want to obtain a single representative sequence from a relatively gappy multiple sequence alignment of ...
- 2,364
2
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1
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501
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Sequence alignment with MUSCLE
For protein multiple sequence alignment (MSA), I am using MUSCLE (v5.1). The default setting without any specifications gives a 'bad' output even though my proteins are very similar (UniProt sequence ...
- 95
-1
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2
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213
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ClustalOmega alignment
I am performing multiple sequence alignment using Clustal Omega for 600 RNA covid-sequences, i.e. cDNA on Genbank, with input characters around 30574 characters for each sequence.
I am running it on ...
2
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4
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2k
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Remove gaps from alignment?
I have an MSA (protein sequence) and I have used various programmes (Clustal, Aliview, MEGA11 etc) to align. However, in all programmes I get many gaps which is not ideal as I am trying to construct a ...
- 105
2
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0
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36
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Alignment with inserts and keeping the indexing of ref seq intact
Parts of sequences are given below-
Reference sequence (pre-alignment):
ATTAAAGGTTTATACCTTCCCAGGTAACAAACCAACCAACTTTCGATCTCTTGTAGATCTGTTCTCTAAACGAACTTTAAAATCTGTGT
...
- 145
4
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0
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257
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How to get phylogenetic tree from multiple genes?
I constructed a phylogenetic tree using a gene (example - secA). I had to gather the same gene sequence for all the required species from public database-NCBI and then constructed the tree after ...
- 73
1
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1
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115
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File format of substitution matrix in clustalw
I need to set the substitution matrix used by command line CLUSTALW when comparing DNA sequences to:
0 -1 -1 -1
-1 0 -1 -1
-1 -1 0 -1
-1 -1 -1 0
from my ...
- 159
1
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1
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171
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Median string problem & multiple sequence alignment
I read about the median string problem as an introduction to the multiple sequence alignment, however none of the MSA algorithms used seems to be using the idea of finding the median string.
To my ...
- 159
2
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2
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98
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Multiple Alignment cost application
Is there any biological application/case where someone would be interested in the estimated total cost of the alignment between a set of sequences (genes or amino acids) without the aligned sequence ...
- 159