Reference-guided De Novo Assembly

Reference-guided de novo assembly approach improves genome reconstruction for related species

AlignGraph github

AlignGraph: algorithm for secondary de novo genome assembly guided by closely related references

Jupyter Notebook

Jupyter Notebook for Beginners: A Tutorial

Family Friends Visiting Recipe May 27, 18

南瓜焖排骨

韭菜炒粉条

番茄紫菜蛋花汤

鲜辣滑糯---芋儿烧鸡

Transposable Elements (TE)

Cited from the paper "Epigenetic interplay between mouse endogenous retroviruses and host genes"

Transposable elements (TEs) are DNA sequences able to move from one chromosome location to another, either through an RNA intermediate (retrotransposons) or simply by excising their DNA copies (DNA transposons). Retrotransposons can be further classified into long terminal repeat (LTR)-containing TEs (LTR retrotransposons and endogenous retroviruses (ERV)) or non-LTR retrotransposons (long and short interspersed nuclear elements, LINEs and SINEs).

IAPs and Early transposon/Mus musculus type D (ETn/MusDs) are two families of mouse ERVs known to be repressed by DNA methylation and are responsible for the majority of new insertional mutations in mice.

RepeatMasker

Design and Use of RepeatMasker

How Do I Install and Use RepeatMasker

Using RepeatMasker to Identify Repetitive Elements in Genomic Sequences

Question: How to make and use a RepeatMasker custom library

Using RepeatMasker

Computational Methods for Finding Repeated Elements

Histone Major Subtypes and Variants

Cited from Wiki "Histone"

"Histones are subdivided into canonical replication-dependent histones that are expressed during the S-phase of cell cycle and replication-independent histone variants, expressed during the whole cell cycle. In animals, genes encoding canonical histones are typically clustered along the chromosome, lack introns and use a stem loop structure at the 3’ end instead of a polyA tail. Genes encoding histone variants are usually not clustered, have introns and their mRNAs are regulated with polyA tails."

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Cited from the Paper "Histone variants: deviants?"

"In most organisms, there are multiple copies of the histone genes encoding for the major histone proteins. These genes are highly similar in sequence, expressed primarily during the S phase of the cell cycle, and code for the bulk of the cellular histones. While histones are among the slowest evolving proteins known, there are nonallelic variants of the major histones that can have significant differences in primary sequence. Some variants have distinct biophysical characteristics that are thought to alter the properties of nucleosomes, while others localize to specific regions of the genome. The variants are usually present as single-copy genes that are not restricted in their expression to the S phase but are expressed throughout the cell cycle. Unlike the major subtypes, the variant genes contain introns and the transcripts are often polyadenylated."

Classical vs Non-classical Monocytes

Cited from Monocyte Wiki

There are at least three types of monocytes in human blood:

1. The classical monocyte is characterized by high level expression of the CD14 cell surface receptor (CD14++ CD16− monocyte)
2. The non-classical monocyte shows low level expression of CD14 and additional co-expression of the CD16 receptor (CD14+CD16++ monocyte).
3. The intermediate monocyte with high level expression of CD14 and low level expression of CD16 (CD14++CD16+ monocytes).

Promoter Proximal, Promoter Distal and Intergenic Peaks

Cited from the Paper "Hira-dependent histone H3.3 deposition facilitates PRC2 recruitment at developmental loci in ES cells"

Promoter distal (−50 kb from TSS to +5 kb from transcription end site (TES) excluding promoter peaks, which is 2 kb around TSSs) or intergenic (all other, excluding promoters) H3K27me3 peaks.

Contacts of HVAC

大东冷暖气工程公司
地址:1000 Grand St., Brooklyn, NY 11211 电话:718-486-9000 

Photo of model and control pad to cliu@goodwillmech.com

开利冷暖气工程公司
地址:88 Jefferson St., New York, NY 11206 电话:718-574-7300

 

Waiting for call back