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LAST: genome-scale sequence comparison

LAST home LAST web service. Recipies for aligning long DNA and RNA reads. LAST finds similar regions between sequences. Get the lastest version: last-926.zip. Try the LAST web service. Sequence data, e.g:. Compare two vertebrate genomes. Align billions of DNA reads to a genome. Of each aligned column. Use sequence quality data properly. Compare DNA to proteins, with frameshifts. Compare PSSMs to sequences. Calculate the likelihood of chance similarities between random sequences. Clone it using Mercurial.

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LAST: genome-scale sequence comparison | last.cbrc.jp Reviews

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LAST home LAST web service. Recipies for aligning long DNA and RNA reads. LAST finds similar regions between sequences. Get the lastest version: last-926.zip. Try the LAST web service. Sequence data, e.g:. Compare two vertebrate genomes. Align billions of DNA reads to a genome. Of each aligned column. Use sequence quality data properly. Compare DNA to proteins, with frameshifts. Compare PSSMs to sequences. Calculate the likelihood of chance similarities between random sequences. Clone it using Mercurial.

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1 cbrc home

2 lacks some features

3 last can

4 handle big

5 indicate the reliability

6 train

7 documents

8 tutorial

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LAST: genome-scale sequence comparison | last.cbrc.jp Reviews

https://last.cbrc.jp

LAST home LAST web service. Recipies for aligning long DNA and RNA reads. LAST finds similar regions between sequences. Get the lastest version: last-926.zip. Try the LAST web service. Sequence data, e.g:. Compare two vertebrate genomes. Align billions of DNA reads to a genome. Of each aligned column. Use sequence quality data properly. Compare DNA to proteins, with frameshifts. Compare PSSMs to sequences. Calculate the likelihood of chance similarities between random sequences. Clone it using Mercurial.

INTERNAL PAGES

last.cbrc.jp

1

LAST Tutorial

http://last.cbrc.jp/doc/last-tutorial.html

LAST finds similar regions between sequences, and aligns them. Example 1: Compare the human and fugu mitochondrial genomes. For our first example, we wish to find and align similar regions between the human and fugu mitochondrial genomes. You can find these sequences in the examples directory: humanMito.fa and fuguMito.fa. We can compare them like this:. Lastdb -cR01 humdb humanMito.fa lastal humdb fuguMito.fa myalns.maf. Less -S myalns.maf. Each alignment looks like this:. The start coordinates are zero...

2

LAST: Genome-Scale Sequence Comparison

http://last.cbrc.jp/doc/last.html

LAST: Genome-Scale Sequence Comparison. LAST finds similar regions between sequences, and aligns them. It is designed for comparing large datasets to each other (e.g. vertebrate genomes and/or large numbers of DNA reads). It can:. Indicate the (un)ambiguity of each column in an alignment. Use sequence quality data in a rigorous fashion. Align DNA to proteins with frameshifts. Compare PSSMs to sequences. Calculate the likelihood of chance similarities between random sequences. You might have to log out an...

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Index of /doc

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last: Summary

http://last.cbrc.jp/last

117;nknown. Mon, 01 Aug 2016 11:12:26 0900. Martin C. Frith. Fixed last-train crash with gap existence cost 0. Martin C. Frith. Made lastal startup yet faster for fastq-versus-fastq. Martin C. Frith. Martin C. Frith. Made lastal startup even faster for fastq-versus-fastq. Martin C. Frith. Made lastal startup faster for fastq-versus-fastq. Martin C. Frith. Martin C. Frith. Bugfix: lastal with -l0 was not reliable, I think. Martin C. Frith. Allowed gap open costs 0. Martin C. Frith. Martin C. Frith.

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LAST tutorial

http://last.cbrc.jp/tutorial

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lh3.github.io

BWA-MEM for long error-prone reads

http://lh3.github.io/2014/12/10/bwa-mem-for-long-error-prone-reads

BWA-MEM for long error-prone reads. A recent paper published by Phil Ashton et al. Has triggered some discussions which subsequently moved to my domain: read mapping. Phil then asked me to clarify how the upcoming bwa-mem works with Oxford Nanopore (ONT) reads. Here we go. Is also using long exact seeds. I then realized that it is also possible for the bwa-mem algorithm to work with PacBio data. With more and more interesting PacBio data sets coming out, I decided to give a try. ONT reads pose new challe...

cbrc.jp

Software | CBRC

http://www.cbrc.jp/cbrc-software

細胞システムの解析 Cellular System Analysis. タンパク質の構造機能予測 Protein Structure/Function Prediction. Life Science DB Integration Web. Http:/ togo.cbrc.jp/. Pairwise alignment of biological. Http:/ www.cbrc.jp/ALN/. RNA secondary structure prediction software. Http:/ www.ncrna.org/centroidfold/. A program to visualize sequence annotation data of the genetic sequence data with graphical layout. Http:/ www.cbrc.jp/GUPPY/. Http:/ last.cbrc.jp/. Multiple sequence alignment program. Http:/ murlet.ncrna.org/. Http:/ griffi...

answermysearches.com

- Answer My Searches

http://www.answermysearches.com/page/2

What is this place? Answers to everything I search for, every day. Mini Searches with Answers. July 27th, 2012 / Author: Greg Pinero (Primary Searcher). These are links associated with recent searches I’ve done. They’re not difficult enough to warrant to their own posts but still super useful. Joinme Free Screen Sharing and Online Meetings. Is this a good free alternative to gotomeeting or copilot? Python snippet for Routing Number Verification Web Service. 8211; Stack Overflow. This explains exactly how...

campagnelab.org

Configure Goby - Campagne Laboratory

http://campagnelab.org/software/goby/configure

Beta version of BWA with Goby support. Uploading a .tsv file with your samples. NYoSh – Not Your ordinary Shell. NYoSh Analysis Workbench 2.0. Running the NYoSh Workbench on Mac. Installation instructions (MetaR 1.3 ). Instructions for Workflow Tutorial. This page describes how to configure Goby. Including goby in your execution PATH. Please note that at this time Goby is compatible with Java6. Compatibility with Java7 will be addressed in a future release. Each mode has its own help, accessible with the...

maoringo.blogspot.com

Maorin Blog: 2月 2011

http://maoringo.blogspot.com/2011_02_01_archive.html

How very little can be done under the spirit of fear. 語のメモ　seqintra meeting (TOM/SAM, sudry, pvalue,refseq,ガンマ分布 etc. General translocase of the outer membrane (TOM complex) and the sorting and assembly machinery (SAM complex), which is dedicated to β-barrel proteins. The SAM. Complex consists of three subunits, Sam35, Sam37, and Sam50, that can associate with a fourth subunit, the morphology component Mdm10, to form the SAM. By http:/ www.jbc.org/content/281/32/22819.full. 12304;仮名】 pち. が 196 以上となる確率.

lh3.github.io

A few comments on GraphMap

http://lh3.github.io/2015/07/30/a-few-comments-on-graphmap

A few comments on GraphMap. Is a new long-read mapper initially tuned for error-prone ONT reads. There are quite a few interesting points methodologically. The following two comments are mostly about techical and practical aspects. Before you read the comments, please bear in mind that I am the developer of BWA-MEM. I could be biased. Comment 1: consensus quality. The most striking point I found in the preprint. And earlier on their website) is that GraphMap significantly outperforms LAST. The general pr...

epigenome.cbrc.jp

Bisulfighter: a pipeline for accurate detection of methylated cytosines and differentially methylated regions — Epigenome Project Portal Site

https://epigenome.cbrc.jp/epigenome/bisulfighter

Genome Browser for Epigenome Project. Galaxy for Epigenome Project. CREST Data Release Policy. CREST IHEC Release 1. Bisulfighter: a pipeline for accurate detection of methylated cytosines and differentially methylated regions. Bisulfighter consists of two parts: (a) mC call part and (b) DMR detection part. Overview of Bisulfighter is presented in Fig.1. The mC call part does genome mapping and mC detection. At the genome mapping phase, it first converts all cytosines of bisulfite-convert...For read mapp...

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last.cbrc.jp

LAST: genome-scale sequence comparison

LAST home LAST web service. Recipies for aligning long DNA and RNA reads. LAST finds similar regions between sequences. Get the lastest version: last-926.zip. Try the LAST web service. Sequence data, e.g:. Compare two vertebrate genomes. Align billions of DNA reads to a genome. Of each aligned column. Use sequence quality data properly. Compare DNA to proteins, with frameshifts. Compare PSSMs to sequences. Calculate the likelihood of chance similarities between random sequences. Clone it using Mercurial.

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