BOL: Related items

SeqFu: A Suite of Utilities for the Robust and Reproducible Manipulation of Sequence Files

Rahul Nayak — Tue, 01 Mar 2022 03:13:33 -0600

A general-purpose program to manipulate and parse information from FASTA/FASTQ files, supporting gzipped input files. Includes functions to interleave and de-interleave FASTQ files, to rename sequences and to count and print statistics on sequence lengths. SeqFu is available for Linux and MacOS.

A compiled program delivering high performance analyses
Supports FASTA/FASTQ files, also Gzip compressed
A growing collection of handy utilities, also for quick inspection of the datasets

Can be easily installed via conda:

conda install -c bioconda seqfu

Address of the bookmark: https://telatin.github.io/seqfu2/

Chemical Elements of Bioinformatics

Rahul Agarwal — Tue, 03 Sep 2013 16:35:39 -0500

You must be familiar with periodic table and colour pattern, but this time you are going to amaze by new elements table by Eagle genomics. Just check it out and have fun :)

http://elements.eaglegenomics.com/

Mulan: MUltiple sequence Local AligNment and conservation visualization tool

Rahul Nayak — Thu, 20 Jul 2017 08:02:32 -0500

Mulan performs multiple (2 or more) sequence alignments with an efficient and rapid "full local" alignment strategy that ensures a recapitulation of evolutionary sequence rearrangements (such as inversions and reshuffling) in any of the species. It combines refine and tba tools to align either "draft" or "finished" quality sequences. Mulan provides a dynamic graphical interface to align and visualize conservation profiles for evolutionarily distant and closely related species.

Input formats, automated data upload from the UCSC Genome Browser, gene annotation, annotation of repetitive elements, and progress report were previously described in the zPicture instructions and we refer the users to these materials for more details. This introduction is mainly focused on some novel features unique to the Mulan.

Address of the bookmark: https://mulan.dcode.org/mulanInstructions.php

Circoletto: visualizing sequence similarity with Circos

Jit — Fri, 09 Feb 2018 10:23:40 -0600

Circoletto, an online visualization tool based on Circos, which provides a fast, aesthetically pleasing and informative overview of sequence similarity search results.

Online version and downloadable software package for offline use (source code in PERL) freely available at http://bat.ina.certh.gr/tools/circoletto/

Contact:ndarz@certh.gr

Address of the bookmark: http://tools.bat.infspire.org/circoletto/

iRNAD: a computational tool for identifying D modification sites in RNA sequence

Abhimanyu Singh — Thu, 16 May 2019 00:20:07 -0500

iRNAD, for identifying D modification sites in RNA sequence. In this predictor, the RNA samples derived from five species were encoded by nucleotide chemical property and nucleotide density. Support vector machine was utilized to perform the classification.

http://lin-group.cn/server/iRNAD/

Address of the bookmark: http://lin-group.cn/server/iRNAD/

Kalign: fast multiple sequence alignment program for biological sequences.

BioStar — Fri, 01 Nov 2019 00:20:41 -0500

Kalign is a fast multiple sequence alignment program for biological sequences.

Align sequences and output the alignment in MSF format:

kalign -i BB11001.tfa -f msf  -o out.msf

Align sequences and output the alignment in clustal format:

kalign -i BB11001.tfa -f clu -o out.clu

Re-align sequences in an existing alignment:

kalign -i BB11001.msf  -o out.afa

Reformat existing alignment:

kalign -i BB11001.msf -r afa -o out.afa

Address of the bookmark: https://github.com/TimoLassmann/kalign

AccessSyRI: finding genomic rearrangements and local sequence differences from whole-genome assemblies

Jit — Sat, 01 Feb 2020 13:38:49 -0600

AccessSyRI: finding genomic rearrangements andlocal sequence differences from whole-genome assemblies

SyRI, a pairwise whole-genome comparison tool for chromosome-level assemblies. SyRI starts by finding rearranged regions and then searches for differences in the sequences, which are distinguished for residing in syntenic or rearranged regions. This distinction is important as rearranged regions are inherited differently compared to syntenic regions.

https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1911-0

Address of the bookmark: https://github.com/schneebergerlab/syri

VICUNA: a software tool that enables consensus assembly of ultra-deep sequence derived from diverse viral or other heterogeneous populations.

biogeek — Tue, 25 Aug 2020 03:40:17 -0500

VICUNA is a de novo assembly program targeting populations with high mutation rates. It creates a single linear representation of the mixed population on which intra-host variants can be mapped. For clinical samples rich in contamination (e.g., >95%), VICUNA can leverage existing genomes, if available, to assemble only target-alike reads. After initial assembly, it can also use existing genomes to perform guided merging of contigs. For each data set (e.g., Illumina paired read, 454), VICUNA outputs consensus sequence(s) and the corresponding multiple sequence alignment of constituent reads. VICUNA efficiently handles ultra-deep sequence data with tens of thousands fold coverage.

http://software.broadinstitute.org/viral/docs/vicuna_v1.0.pdf

Address of the bookmark: https://www.broadinstitute.org/viral-genomics/vicuna

A web-based tool for sequence alignment statistics and innovative visualization

BioStar — Thu, 04 Apr 2024 01:44:50 -0500

AlignStatPlot, a new R package and online tool that is well-documented and easy-to usefor MSA and post-MSA analysis. This tool performs both traditional and cutting-edge analy-ses on sequencing data and generates new visualisation methods for MSA results. Whencompared to currently available tools, AlignStatPlot provides a robust ability to handle andvisualise diversity data, while the online version will save time and encourage researchersto focus on explaining their findings. It is a simple tool that can be used in conjunction withpopulation genetics software (PDF) AlignStatPlot: An R package and online tool for robust sequence alignment statistics and innovative visualization of big data.

Address of the bookmark: https://bioinformatics.um6p.ma/AlignStatPlot/

MetaPred2CS

Manisha Mishra — Fri, 03 Mar 2017 05:15:07 -0600

MetaPred2CS Web server is a meta-predictor based on Support Vector Machine (SVM) that combines 6 individual sequence based protein-protein interaction prediction methods to predict prokaryotic two-component system protein-protein interactions (PPIs). The methods implemented in MetaPred2CS are 2 co-evolutionary methods: in-silico two hybrid (i2h) and mirror tree (MT) methods and 4 genomics context based methods: phylogenetic profiling (PP), gene fusion (GF), gene neighbourhood (GN) and and gene operon methods (GO).

http://metapred2cs.ibers.aber.ac.uk/

Address of the bookmark: https://github.com/martinjvickers/MetaPred2CS