Jul
10
comment How to combine multiple files into one file?
Equivalently answered here assuming OP wants to concatenate vertically, not horizontally, though the approach could be modified anyway: stackoverflow.com/questions/18695105/…
Apr
4
answered Phyre2 vs ITasser, completely different models generated
Apr
1
comment Plot a circos plot to show the consistency between 2 samples
FWIW, I've never found a use case where a Circos plot was the best visualisation tool. They look pretty, but they don't really convey much information.
Jan
20
awarded  Announcer
2018
Dec
24
comment Annotation with Prokka or RAST.
Prokka can do viruses, but you may want to change which translation table it uses to get better blast results
Dec
22
comment Truncating branch length values of Phylogenetic tree with biopython
Can you provide an example of your input tree? I’d approach this my parsing the treefile itself, truncating the values, writing a new tree, and then plotting that, rather than trying to do it whilst plotting. BioPython’s tree handling is not its strong suit IMO, so for something like this I would probably use ETE3 or Dendropy - those tools may include options for truncating your node/branch values.
Dec
11
answered Importing GFF file with Biopython
Sep
10
comment How to iterate protein sequences using amino acids?
Cross posted at Biostars: biostars.org/p/336237/#337089
Jul
30
comment Using a Bash Script to search TaxIDs against NCBI's Taxonomy yields “400 Bad Request” error?
Aside from your specific question slightly, you might be interested in looking at the NCBITaxa() tool in the ETE3 package. It basically does what your script does, but provides lots of other useful methods for querying the ncbi taxa database.
Jun
21
awarded  Yearling
Apr
5
comment I need to use my code with fasta format. Can anybody help?
If you’re on windows 10, install the Bash on Ubuntu application that was released as part of the anniversary update a few months ago. It essentially gives you a full Unix virtual machine on windows, and integrates quite nicely. Save yourself a lot of headaches in the future and switch to unix based systems ASAP.
Apr
3
comment I need to use my code with fasta format. Can anybody help?
You can use it for both reading in amd writing out your sequences in a preformatted FASTA format. There is rarely a good reason to write your own fasta parser.
Apr
2
comment I need to use my code with fasta format. Can anybody help?
Use BioPython for this with SeqIO.write
2017
Nov
16
answered How to find the sum of all sequences in a multifasta file
Nov
16
answered How to determine a protein's cellular location based on its sequence?
Oct
30
answered Mutations in sequences relative to reference (histogram)
Oct
27
comment Chimera Alignments
You are probably looking for the “Morph Conformations” function within Chimera. It’ll move and superimpose 2 structures on to one another.
Oct
27
comment Mutations in sequences relative to reference (histogram)
Do you just want a graphical representation of the diverse regions of a multiple sequence alignment?
Aug
7
comment How can I edit a specific FASTQ read in place, given the read ID?
Just out of curiosity, why do you need to edit your reads?
Jul
18
comment changing blast parameters using NCBIWWW module
Have you checked the hits you're getting back from BLAST in your different methods? If your query matches the same few high-scoring sequences regardless of algorithm, you'll then be creating an MSA of exactly the same sequences each time (maybe +/- some random seeding noise) which would mean your graph was the same.