sonbion.blogg.se - Python dna sequence analysis

PYTHON DNA SEQUENCE ANALYSIS SOFTWARE
PYTHON DNA SEQUENCE ANALYSIS FREE

Sequence conversion Provided by - a lot of conversion choices with easy interface.

I used it as part of my workflow to get closer to special NEXUS format (or intermediate) for performing maximum likelihood phylogenetic analysis of large sets of sequences.

ALTER (ALignment Transformation EnviRonment) - complex interface but offers lots of options for output.

The launched notebooks illustrate ways to easily work with the output in Python. That page also links to the main Circos resources there. Circos so it is actively available in a browser with one click to launch Jupyter environment for Circos via Binder.

Circos on Jupyter - Circos in your browser-based Jupyter enviroment served from.

That page also links to the main BLAST resources there.

Blast-binder - Launchable Jupyter environment for running command line-based BLAST via Binder.

That page also links to the main MUSCLE resources there.

Muscle-binder - Launchable Jupyter environment for running command line-based Muscle via Binder.

Looks like it does protein sequence analysis too and working with PDB files.

PYTHON DNA SEQUENCE ANALYSIS FREE

ProDy Project - "ProDy is a free and open-source Python package for protein structural dynamics analysis".ProViz - a web-based visualization tool to investigate the functional and evolutionary features of protein sequences.g:Profiler - for characterizing and manipulating gene lists of high-throughput genomics.

T-profiler - for scoring the activity Of pre-defined groups of yeast genes using gene expression data **As of May 2016 it was not accepting uploads.**.PrePPI: database of predicted and experimentally determined protein-protein interactions (PPIs) for yeast and human.PaxDb: Protein Abundance Across Organisms.

PYTHON DNA SEQUENCE ANALYSIS SOFTWARE

Nucleobytes - DNA editor and 4peaks sequence chromatogram viewer along with other mac software.

"form allows you to assemble a set of contiguous sequences (contigs) with the CAP3 program. CAP3 Sequence Assembly Program - online, webserver for making contigs from DNA sequences.The finished DNA sequences can then be exported to common sequence file formats, such as FASTA. SeqTrace can automatically identify, align, and compute consensus sequences from matching forward and reverse traces, filter low-quality base calls, and perform end trimming of finished sequences. SeqTrace makes it easy to quickly generate high-quality finished sequences from a large number of trace files. SeqTrace- "is an application for viewing and processing DNA sequencing chromatograms (trace files).Genomicus: Genomes in Evolution - "genome browser that enables users to navigate in genomes in several dimensions: linearly along chromosome axes, transversaly across different species, and chronologically along evolutionary time.".Archaeopteryx for the visualization of annotated phylogenetic trees.MUSCLE: MUltiple Sequence Comparison by Log-Expectation.Links to many EMBOSS portals, servers and mirrors under 'Servers'.`cons` alignment consensus program and many others at EMBOSS explorer website.Biotools at UMASS MED (formerly included EMBOSS.Sequence Manipulation Suite: Restriction Map - has at the left side links to other tools they have.20 Installable software for fine-tuning sequence alignments.16 For genomic arrangement (synteny) comparisons/Fungal Genomics Resources.14 Nucleic acid system building and DNA structure design.11 Some sequence analysis but mostly OTHER.8 Extract physico-chemical data from Protein or DNA sequences.