User: little_more

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Posts by little_more

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How to find a number of TE in a set of genomes?
... I have a list of assemblies IDs (GenBank) and a list of corresponding chromosomes and plasmids. A toy example: a = [GCA_000005845.2, GCA_000006925.2, GCA_000007405.1, GCA_000007445.1, ...] b = [CP024720.1, CP024722.1, CP024721.1, LT601384.1, LT838196.1,...] I'd like to find a number of IS i ...
genome biopython written 22 hours ago by little_more0
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Counting a number of mobile elements in a list of genomes using BioPython
... Suppose I have a big list of assembly IDs: ['GCA_000005845.2', 'GCA_000006925.2', 'GCA_000007405.1', 'GCA_000007445.1', ...] And I need to count a number of mobile elements in each chromosome in all assemblies. How could I do this using BioPython? It seems that I need to download all genba ...
genome biopython written 2 days ago by little_more0
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MGRA returns error
... I'm using MGRA server (http://mgra.cblab.org/) to reconstruct rearrangement history but it returns an error. I hope someone here has used this server and knows what is wrong. Grimm file: > GCA_000027125.1 -4 +33 -36 +29 -23 +27 -20 +5 -18 -9 +21 -32 -2 -16 +3 -31 -14 +39 -38 +11 -30 +13 ...
software error mgra written 4 weeks ago by little_more0 • updated 4 weeks ago by RamRS20k
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How to get a strain name if I know only an assembly ID?
... Suppose I have a tree with assembly IDs of different E.coli strains in it (all from NCBI). Is there any common way to replace each assembly ID with the corresponding strain name? I tried using BioPython (efetch) but it raises an error. ...
assembly written 4 months ago by little_more0 • updated 4 months ago by vkkodali980
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Comment: C: How to get fasta sequences for CDS if I have proteins IDs?
... Thank you! But is it possible to use the command for > 500 IDs? Documentations says 'a comma-delimited list of UIDs may be provided... but if more than about 200 UIDs are to be provided, the request should be made using the HTTP POST method'. ...
written 5 months ago by little_more0
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Comment: C: How to get fasta sequences for CDS if I have proteins IDs?
... IDs are from different genomes. In fact, I have a table with protein IDs: group1 group2 group3 group4 ... bac1 ID1 ID2 ID3 ID4 bac2 ID5 ID6 ID7 ID8 bac3 ID9 ID10 ID11 ID12 ... and I need ...
written 5 months ago by little_more0
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Comment: C: How to get fasta sequences for CDS if I have proteins IDs?
... Oh, my bad. All IDs are from GenBank *Escherichia* genome assemblies (.faa files). For example, AAN78512.1, BAB33431.1, BAB33432.1. P.S. I know that I can simply go to NCBI and get CDS for each protein manually but the question is how to do this for a large number of ID groups. I've heard somethin ...
written 5 months ago by little_more0
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How to get fasta sequences for CDS if I have proteins IDs?
... I have a large table where each column contains protein IDs of a particular group of orthologs. How do I map these protein IDs to gene IDs and then get a file with fasta sequences of all genes for each column? ...
gene sequence written 5 months ago by little_more0 • updated 5 months ago by h.mon24k
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Comment: C: Correlation of expression and compartmentalization
... Well, thank you for the link, but the question was actually about the way to estimate correlation. Moreover, how to use a .bigwig file for that? ...
written 12 months ago by little_more0
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Comment: C: Correlation of expression and compartmentalization
... k562, for example. I'd like to compute Spearman correlation as in the Liberman-aiden paper. ...
written 12 months ago by little_more0

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