http://gmod.org/wiki/MAKER_Tutorial 简单好用 identify repeats, to align ESTs and proteins to the genome, and to automatically synthesize these data into feature-rich gene annotations, including alternative splicing and UTRs, as well as attributes such as…
(Gene prediction and comparison) 使用基于基因组序列的从头预测方法(Ab initio methods)(同时分别使用头预测软件( GENSCAN和 AUGUSTUS)和预测exon和intron的剪切位点.)和基于证据支持的基因预测(Evidence-based methods)(与dog和human比较).得到不同基因座数目.最后做了一个panda的参考基因集. (measure the quality of gene prediction):通过比较不同…
原文:http://homepages.ulb.ac.be/~dgonze/TEACHING/bioinfo_glossary.html Affine gap costs: A scoring system for gaps within alignments that charges a penalty for the existence of a gap and an additional per-residue penalty proportional to the gaps length…
准备读四篇denovo的文献: Nature Biotechnology(2015) - Sequencing of allotetraploid cotton (Gossypium hirsutum L. acc. TM-1) provides a resource for fiber improvement Whole-genome sequencing of the snub-nosed monkey provides insights into folivory and evolutio…
与最大熵模型相似,条件随机场(Conditional random fields,CRFs)是一种机器学习模型,在自然语言处理的许多领域(如词性标注.中文分词.命名实体识别等)都有比较好的应用效果.条件随机场最早由John D. Lafferty提出,其也是Brown90的作者之一,和贾里尼克相似,在离开IBM后他去了卡耐基梅隆大学继续搞学术研究,2001年以第一作者的身份发表了CRF的经典论文 "Conditional random fields: Probabilistic models f…
