Team:Shenzhen BGIC 0101/Tutorial/neochr




NeoChr module would assist users to grab related genes in different pathways manually, to rewire genes’ relationship logically*, and to replace genes with ortholog that score higher*. Firstly, it would allow users to define gene order and orientation in DRAG&DROP way. Secondly, decoupled these genes if have overlap and make all genes are non-redundancy. Finally, add chromosome features to build a new chromosome and show in the JBrowse. Moreover, users can drag a window in the JBrowse and delete any gene in the window.
*These function are unavailable now, please wait for version 2.
**You can also add any thing here including your own water mark.

Plugin Scripts

This module contains three plugins:, and


This plugin is to decouple the genes which have overlap gene regions. These overlapping genes can be decoupled if meet the following conditions: (1)If two genes have overlap gene regions, the latter gene 5’UTR does not cover the former gene initial codon (ATG); (2)Overlapping region initial coordinate is in the coding DNA sequences(CDS) of gene which is need to be decoupled; (3)The decouple site of CDS have synonymous substitute codon to replace; After decoupling, we use these non-redundancy genes to generate a GFF file and a FASTA file.

1.1.1 Internal operation

First, this plugin extracts base sequence from the genome file according to the gene order list, and records the gene order in the list. And then plugin records the annotation information according to the specie GFF file, moreover, plugin extends gene CDS upstream 600bp as 5’-UTR and downstream 100bp as 3’-UTR if the GFF file does not contain annotated these two features.
Second, this plugin detects the overlapping genes in the same chromosome. In case the overlapping genes are detected, it will judge whether the overlapping initial site is located in the CDS region, and identify the site is belong to phase0/1/2.
Third, the plugin attempts to synonymous substitute codon to break the initial codon intra the CDS. Printing information whether or not be decoupled successfully, such as:
And non-redundancy genes are generated.
Finally, the plugin links non-redundancy genes to construct a new chromosome according to the gene order.

1.1.2 Example

We have two input forms to execute the plugin:
1. Using string format as gene order list input form:
perl --species saccharomyces_cerevisiae_chr --list_format string --gene_order="YAL054C -,YAL038W +,YBR019C -,YBR145W +,YCL040W +,YCR012W +,YCR105W +,YDL168W +,YPL017C -,YIL177C -,YIL177W-A +,YIL172C -,YIL171W-A +,” --geneset_dir ../gene_set --upstream_extend 600 --downstream_extend 100 --neo_chr_gff neochr.gff --neo_chr_fa neochr.fa
2. Using file format as gene order list input form:
erl --species saccharomyces_cerevisiae_chr --list_format file --gene_order gene_ordre.list --geneset_dir ../gene_set --upstream_extend 600 --downstream_extend 100 --neo_chr_gff neochr.gff --neo_chr_fa neochr.fa

1.1.3 Parameters

Parameter Description
list_format set the input form of gene order list string string/file
gene_order set the input gene order list file(include pathway genes and addition genes)
Parameter Description Default Selectable range
geneset_dir set the species annotation directory 600
upstream_extend set the length of gene downstram(bp) 100
neo_chr_gff set the name of output neochr gff file
neo_chr_fa set the name of output neochr fasta file
help Show help information

1.1.4 The format of output file

The output files are standard GFF and FASTA format files which are decoupled.

1.decoupled GFF file



2.decoupled FASTA file



This plugin will add the LoxPsym sequence and the customized left and right telomeres, centromere and autonomously replicating sequence (ARS) into the FASTA file and GFF file which are generated by

1.2.1 Internal operation

The plugin adds LoxPsym behind the first 3bp of 3’-UTR in each gene and adds telomere, centromere and ARS according this mode:
left_telomere + gene1 + centromere + gene2 + ARS + gene3 + right_telomere
The distance between centromere and ARS is less than 30Kb.
Finally, user can see the new added features chromosome according to the JBrowse.

1.2.2 Example

perl --loxp loxPsym.feat --left_telomere UTC_left.feat --right_telomere UTC_right.feat --ars chromosome_I_ARS108.feature --centromere chromosome_I_centromere.feat --chr_gff neochr.gff --chr_seq neochr.fa --neochr_seq --neochr_gff

All the feature file format is 4 lines format, for example:
  name = site_specific_recombination_target_region
  type = loxPsym
  source = BIO
Note: the first line is the detail name of feature, the second line is the type of feature, the third line is the source of feature and the last line is the sequence of feature.

1.2.3 Parameters

Parameter Description Default Selectable range
left_telomere set the sequence of left telomere
right_telomere set the sequence of right telomere
chr_gff set the input neorchr_gff file
chr_seq set the input neorchr_gff file
neochr_seq set the name of output added loxps and telomeres neochr_fa file
neochr_gff set the name of output added loxps and telomeres neochr_gff file

1.2.4 The format of output

The output files are standard GFF and FASTA format of adding features chromosome.
1. added features GFF file



This plugin can modify the GFF and FASTA file which are generated by according to the user drags a window in the JBrowse and delete any gene in the window.

1.3.1 Internal operation

Firstly, user uses mouse to drag a window in the added features FASTA file which is showed in the JBrowse and JBrowse displays all the genes in this window.Secondly, user decides which genes is need to be delected from the new chromosome and plugin deletes genes from GFF file and modify FASTA in the same time.

1.3.2 Example

perl --delete="YAL054C,YAL038W" --neochr_gff --neochr_fa --slim_gff neochr.refine.delete.gff --slim_fa neochr.refine.delete.fa

1.3.3 Parameters

Parameter Description Default Selectable range
delete Set the to be deleted gene list
neochr_gff Set the input GFF file which is generated by
neochr_fa Set the input FASTA file which is generated by
slim_gff Set the output GFF file
slim_fa Set the output FASTA file

1.3.4 The format of ouput

The output files are standard GFF and FASTA format of deleted genes chromosome.