Question: I need to understand how to convert a GBK and FAA files to the files that Circos accepts.
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gravatar for maxwells_daemon
15 days ago by
maxwells_daemon0 wrote:

I need help understanding how to convert these file types to the template that Circos accepts. Please comment and I will provide more detail. Thank you.

The types of files Circos accepts are of the following notation:

chr - hs1 1 0 247249719 green
chr - hs2 2 0 242951149 green
chr - hs3 3 0 199501827 green
chr - hs4 4 0 191273063 green
chr - hs5 5 0 180857866 green
chr - hs6 6 0 170899992 green
chr - hs7 7 0 158821424 green
chr - hs8 8 0 146274826 green

This is the data types I have:

FAA file:

>ORF1_1 seq1 2300..2602 DNA binding protein 
MSNKYPVAYAVGQKIKSLRKSQGYTVFQLAKEIDISEQQLFRYERGVNRIDIDCLVKVLDVLGINIGNFF
EDVMGGMVDVPENNEQHIPAHFDNKALSIF

PTT file:

Location    Strand  Length  PID Gene    Synonym Code    COG Product
2300..2602  +   100 1834182688  -   ORF1_1  -   -   DNA binding protein 
3171..3938  -   255 1834182689  -   ORF1_2  -   -   Hydrogen sulfide production: membrane anchoring protein 
3935..4513  -   192 1834182690  -   ORF1_3  -   -   Molybdopterin oxidoreductase, Psr/Psh family, PsrB-like Fe-S subunit 
4528..6807  -   759 1834182691  -   ORF1_4  -   -   Thiosulfate reductase 
7589..8392  -   267 1834182692  -   ORF1_5  -   -   Conserved protein YunE

.txt file for antitoxins and toxins:

Location    Strand  ID  Gene    Locus_tag   Length(aa)  Type    blastp_subject  subject_domain  subject_family  blastp_identity blastp_evalue   h_value query_annotation    subject_annotation
637603..637929  -   ORF13_1 -   ORF13_1 108 toxin   197287170   RelE    relE-like_domain    97.22   2e-74   97.22   Plasmid stabilization system protein    plasmid stabilization protein [Proteus mirabilis HI4320]
637935..638204  -   ORF13_2 -   ORF13_2 89  antitoxin   197287171   PHD PHD-like_domain 97.75   9e-58   97.75   Antitoxin   antitoxin [Proteus mirabilis HI4320]
***

How do I convert the files of these types to the other in a way that Circos accepts and makes sense?

ADD COMMENTlink modified 11 days ago • written 15 days ago by maxwells_daemon0

Comment to provide more detail. Please elaborate on the format you need.

ADD REPLYlink modified 14 days ago • written 14 days ago by WouterDeCoster29k

Well, what do you want to show?

ADD REPLYlink written 11 days ago by jrj.healey4.6k

I want to show an outer ring with the genome, inner ring with aligned toxin-antitoxin pairs, and prophage regions. I used CGView before, but I need to use Circos.

ADD REPLYlink written 11 days ago by maxwells_daemon0
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