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
Thursday 31 May 2018
Wednesday 30 May 2018
Saturday 26 May 2018
Tuesday 22 May 2018
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.
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.
Monday 21 May 2018
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."
"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."
Thursday 17 May 2018
Classical vs Non-classical Monocytes
Cited from Monocyte Wiki
There are at least three types of monocytes in human blood:
There are at least three types of monocytes in human blood:
- The classical monocyte is characterized by high level expression of the CD14 cell surface receptor (CD14++ CD16− monocyte)
- The non-classical monocyte shows low level expression of CD14 and additional co-expression of the CD16 receptor (CD14+CD16++ monocyte).
- The intermediate monocyte with high level expression of CD14 and low level expression of CD16 (CD14++CD16+ monocytes).
Wednesday 16 May 2018
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.
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.
Wednesday 2 May 2018
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
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
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
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