|
||||||
|
ELPH : Estimated Locations of Pattern Hits Overview ELPH is a general-purpose Gibbs sampler for finding motifs in a set of DNA or protein sequences. The program takes as input a set containing anywhere from a few dozen to thousands of sequences, and searches through them for the most common motif, […] Next Generation Sequencing (NGS) is a frequently applied approach to detect sequence variationsbetween highly related genomes. Recent large-scale re-sequencing studies as the Human 1000 GenomesProject utilize NGS data of low coverage to afford sequencing of hundreds of individuals. Here, SNPsand micro-indels can be detected by applying an alignment-consensus approach. However,computational methods capable of […] Description ANNOVA is an efficient software tool to utilize update-to-date information to functionally annotategenetic variants detected from diverse genomes. Given a list of variants with chromosome, startposition, end position and observed nucleotides, ANNOVAR can identify whether SNPs or indels causeprotein coding changes and what is the amino acids that were changed, or identify variants […] http://abacas.sourceforge.net/index.html ABACAS is intended to rapidly contiguate (align, order, orientate), visualize and design primers to close gaps on shotgun assembled contigs based on a reference sequence.
ABACAS uses MUMmer to find alignment positions and identify syntenies of assembled contigs against the reference. The output is then processed to generate a pseudomolecule taking overlapping […] ABBA From amos Jump to: navigation, search ABBA: Assembly Boosted By Amino acid sequences Contents [hide] 1 Overview 2 Download 3 References 4 Acknowledgements Overview Assembly Boosted By Amino acid sequence is a comparative gene assembler, which uses amino acid sequences from predicted proteins to help build a better assembly. see the journal paper. […] samtools mpileup -uf ref.fa aln.bam | bcftools view -cg – | vcfutils.pl vcf2fq > cns.fq #!/usr/bin/perl -w use strict; use Bio::SeqIO; use Bio::Seq::Quality; use Getopt::Long; die “pass a fasta and a fasta-quality file\n” unless @ARGV; my ($seq_infile,$qual_infile) = (scalar @ARGV == 1) ?($ARGV[0], “$ARGV[0].qual”) : @ARGV; ## Create input objects for both a seq (fasta) and qual file my $in_seq_obj = Bio::SeqIO->new( -file => $seq_infile, -format => ‘fasta’, ); my […] Use the built-in “samtools sort” command rather than a generic sort. Samtools sort works on BAM files so you should convert your alignments to BAM format using samtools view -bS filename.sam > filename.bam samtools sort filename.bam sorted samtools index sorted.bam This ofcourse assumes you have generated the SAM file using method (1). The file “sorted.bam” […] Welcome to the CCMAR Computational Cluster Facility: GYRA – gyra.ualg.pt¶ The GYRA cluster facility is administered and maintained by Cymon J. Cox of the Plant Systematics and Bioinformatics Research Group (PSB). System:¶ The GYRA cluster facility consists of: Frontend: 16-core 2.3GHz 32GB DELL PowerEdge R715 compute-0-0: 8-core 2.6GHz 8GB DELL PowerEdge SC1435 compute-0-1: 8-core […] Bacteria Gene Prediction * GeneMark and Glimmer This provides the foundation for operon predictions and promotor predictions. One way to verify the gene prediction result is to check the presence of Shine-Dalgarno sequence in fron of each gene which is a purine-rich region with a consensus AGGAGG and is located within 20 bp upstream of […] |
|
||||
|
Copyright © 2025 小生这厢有礼了(BioFaceBook Personal Blog) - All Rights Reserved Powered by WordPress & Atahualpa |
||||||
Recent Comments