Analysis of gene family characteristics - chromosome location analysis

1 The concept of chromosome location analysis

   Chromosomal mapping analysis is to mark the positions of gene family members on chromosomes , Observe whether the members of the gene family are clustered on the chromosome .

2 Analysis tools

2.1 MG2C(MapGene2Chromosome)

  MG2C It is an online analysis tool , Address the following ：

http://mg2c.iask.in/mg2c_v2.0/

2.1.1 Input file

   There are two dialog boxes at the top of the page , Fill in on the left 4 Column tab separated matrix , From left to right , Take this as ：GeneID、 The starting position 、 Termination position and chromosome number , These data can be obtained from annotation files assembled to the chromosome level .

2.1.2 Output results

   Click on DRAW Button , You can draw , The generated image can be exported as .svg Format , Subsequent reuse Ai Make changes .

2.1.3 Parameters change

   In the picture drawn , Chromosome id The font of 、 The font size and other details are modified through the option box on the left of the page .

2.2 TBtools

  TBtools It is a powerful graphical operation based on Windows、Mac Shengxin analysis software developed by operating system , Below are references GB/T 7714 Format .

Chen C, Chen H, Zhang Y, et al. TBtools: an integrative toolkit developed for interactive analyses of big biological data[J]. Molecular plant, 2020, 13(8): 1194-1202.

   The development of literature DOI by https://doi.org/10.1016/j.molp.2020.06.009

   Choose... From the menu bar Graphics, Then select Show Genes on Chromosome, choice Gene Location Visualize from GTF/GFF.

2.2.1 Input file

1. .gff Annotate Document ;
2. What you want to show Gene, Conserve genes ID Single column matrix of （ gene ID Can be with gff Column 9 of the document GeneID Corresponding ）;
3. Duplicate gene pairs , Conserve genes ID A matrix with two columns separated by tabs （ The two gene sequences in each row are basically the same , That is, there are two copies of the same gene on the chromosome ）;
4. Gene rename , take gff In the comment file GeneID Change it to the name you want , Tab separated two column matrix ;
5. Gene color , Save a two column matrix separated by tabs , The first column is Gene rename , The second column is the decimal color code ;
6. Document of gene density on chromosome , adopt TBtools Of Sequence Toolkit Under the menu bar GFF3/GTF Manipulate Under the options bar Gene Density Profile function , Pass in .gff file , Modify the division of chromosomes bin Can generate .

   Above 6 In a file ,1 and 2 Is a must ,3-6 It's optional .

2.2.2 Output results

   The generated results are shown in the figure above , Under this window , Modify chromosome width 、 The proportion of the picture display and so on , Click on the Save Graph, Generate according to your own needs .png、.jpg、.svg Equiform .

2.2.3 final result

   Reuse Ai Add a legend , Marking the gene density corresponding to different colors is perfect .