Annotation Coordinates

1-based

software: 1). samtools; 2). annovar; 3). stringtie (gtf file,gene_abundance file);

file format:
1). vcf:只有第二列为POS信息;
2). sam/bam:只有第四列为POS信息;
3). gff (闭区间):第四列和第五列给定开始和结束
1. gff格式还要注意其strand(正负链)和phase(要从该feature开头移走的碱基个数)
2. 这个维基百科网页(https://en.wikipedia.org/wiki/General_feature_format)在说和bed一样为half-open(半开),估计误导了一大片人。
4). the Description of Sequence Variants (nomenclature)
5). gencode: 第四列和第五列给定开始和结束
6). ANNOVAR input file

0-based

software:

file format:
1). bed(左闭右开):
1. 注意给strand
2. 第二列和第三列给定开始和结束 (比如3 5,包含的是第4个碱基到第5个碱基之间的序列[这里的第4和第5是在1-based的坐标语境中],一共2个碱基);

 

HOX gene

ref: 2013-the regulation of hox gene expression during animal development

 

homeosis the replacement of part of one segment of an insect or other segemented animal by a structure characteristic of a different segment, especially through mutation.
homeobox any of a class of closely similar sequences which occur in various genes and are involved in regulating embryonic development in a wide range of species