Shulou(Shulou.com)06/02 Report--

How to use the R language package RIdeogram to display the results of blast double sequence alignment. In view of this problem, this article introduces the corresponding analysis and solution in detail, hoping to help more partners who want to solve this problem to find a more simple and feasible method.

RIdeogram is an R language package used to show idiogram, such as the density distribution of snp, the distribution of certain genes on chromosomes, and so on.

The published paper is

RIdeogram: drawing SVG graphics to visualize and map genome-wide data on the idiograms PeerJ 2020

Several data collection codes are also provided in the attachment, which is a very good learning material.

When I looked at the help documentation for this package, I also found a diagram showing two or three genome collinearity analyses.

The data you need to prepare are two data boxes.

The first is the basic information of the genome, including

> head (karyotype_dual_comparison)

Chr Start End fill species size color

1 I 1 23037639 969696 Grape 12 252525

2 II 1 18779884 969696 Grape 12 252525

3 III 1 19341862 969696 Grape 12 252525

4 IV 1 23867706 969696 Grape 12 252525

5 V 1 25021643 969696 Grape 12 252525

6 VI 1 21508407 0ab276 Grape 12 252525

The second is the result of collinear analysis.

> head (synteny_dual_comparison)

Species_1 Start_1 End_1 Species_2 Start_2 End_2 fill

1 1 12226377 12267836 2 5900307 5827251 cccccc

2 15 5635667 5667377 17 4459512 4393226 cccccc

3 9 7916366 7945659 3 8618518 8486865 cccccc

42 8214553 8242202 18 5964233 6027199 cccccc

5 13 2330522 2356593 14 6224069 6138821 cccccc

6 11 10861038 10886821 10 8099058 8011502 cccccc

With an understanding of the basic data entry format, we can convert the blast comparison results into this form.

The first is to use blast comparison to build the database.

Makeblastdb-in mt.fasta-dbtype nucl-out mt

Comparison

Blastn-query cp.fasta-db mt-outfmt 6 > output.txt

Construct the input data of RIdeogram

Df1.txt file content

Chr,Start,End,fill,species,size,color

I,1,131478,FF9D1E,chloroplast,12,252525

I,1,444567,FF9D1E,mitochondrion,12,252525

Output6.txt file content

NC_044701 NC_044768 96.76 1603 43 7 54477 56074 375799 374201 0.0 2663

NC_044701 NC_044768 83.69 423 37 19 68192 68587 44003 44420 2e-101 370

NC_044701 NC_044768 85.28 326 38 5 66335 66654 360145 360466 1e-88 327

NC_044701 NC_044768 74.07 891 172 45 102938 103801 332888 333746 1e-83 311

NC_044701 NC_044768 90.54 148 11 3 36180 36324 64144 64291 4e-48 193

NC_044701 NC_044768 95.56 90 3 1 49 138 406657 406745 4e-33 143

NC_044701 NC_044768 96.51 86 2 1 110947 111032 420751 420667 2e-32 141

NC_044701 NC_044768 96.43 843 0 31738 31821 384266 384349 5e-32 139

NC_044701 NC_044768 94.94 79 4 0 53913 53991 2926 3004 2e-27 124

NC_044701 NC_044768 96.77 62 2 0 105594 105655 110375 110314 2e-21 104

NC_044701 NC_044768 87.34 79 6 3 88210 88284 240028 240106 2e-16 87.9

NC_044701 NC_044768 100.00 31 00 10365 10395 63403 63373 2e-07 58.4

NC_044701 NC_044768 96.97 330 1 66299 66330 360093 360125 2e-06 54.7

Drawing code

Df1

Welcome to subscribe "Shulou Technology Information " to get latest news, interesting things and hot topics in the IT industry, and controls the hottest and latest Internet news, technology news and IT industry trends.