10 请问在自己进行手动比对鉴定基因家族的时候最正确的做法是什么?

老师好,我研究的基因家族通过咱们课程的方法没有鉴定完全,我看文章里用手动tblastn比对,根据比对结果在genewise网站里进行外显子的预测,然后手动查找起始终止密码子。我在tblastn后出现一条query比对上基因组的多条染色体的多段序列,请问这种情况应该怎么取舍呢?提取比对结果最好的还是都提取出来最后比对完再删除呢?还有个问题就是genewise比对以后需要手动去找起始、终止密码子吗?我看文章里有的没找,但是有的列出来的基因家族都是有起始和终止密码子的。

请先 登录 后评论

2 个回答

omicsgene - 生物信息
擅长:重测序,遗传进化,转录组,GWAS

你的基因组注释的基因可能不好,这种的只能手动调整; 

blast比对也是比对蛋白序列,你比对基因组染色体是不对的

请先 登录 后评论
Mr.Black

确实有可能有很多基因没有注释出来,所有才要对基因组核酸序列进行比对啊。MER上发的很多昆虫基因组文章都是先对基因组注释,然后再手动注释目标基因家族,我看了很多鉴定解毒和化学感受相关基因家族的文章里基本都是这样写的:For analysis of the OR and P450 gene families, we collected T.castaneum P450 and all known Coleopteran OR protein sequences from previously published papers (Mitchell et al., 2020; Zhu et al., 2013). Pseudogenes were removed manually and the remaining protein sequences were used as queries in tblastn (blast version 2.9.0+) searches (E-value =1e-5) against the H. axyridis genome to find candidate genes. genewise version 2.4.1 was used to detect the gene structure (Birney et al., 2004). Then we used hmmer version 3.1b2 to perform searches against the Pfam database to confirm the identity of the candidate genes (Finn et al., 2014; Potter et al., 2018). For P450 candidate genes we used the p450 (PF00067) HMM profile, and for OR candidate genes we used the 7tm_6 (PF02949) or 7tm_4 (PF13853) HMM profile. The sequences containing the HMM profiles were regarded as confirmed genes. To identify more candidate OR genes, we carried out HMM pattern scans using hmmer version 3.1b2 at genome level without homology searching function. The identified candidate genes were merged with those identified by homology searching at the protein level.  https://doi.org/10.1111/1755-0998.13342

所以我现在用hmmer搜索的方法鉴定出来45个,但是金源物种一般都是60-70个,所以我想知道怎么才能尽可能多的找到目标基因家族成员

请先 登录 后评论
  • 2 关注
  • 0 收藏,176 浏览
  • Mr.Black 提出于 2024-03-27 20:54

相似问题