The study of Protein–Protein Interactions (PPIs) has a crucial role in biology, medicine and the pharmaceutical industry. PPIs can be investigated from two aspects: The interaction partners of a specific protein and the amino acid residues...
How to download FASTA sequence for certain gene features while in the NCBI's Sequence Viewer.
Sequence Viewer homepage:
www.ncbi.nlm.nih.gov/projects/sviewer/
Sequence Viewer playlist:
https://www.youtube.com/playlist?list=PL76D7EE6A6A8AC1C3
platanus.bio.titech.ac.jp - Platanus is a novel de novo sequence assembler that can reconstruct genomic sequences of highly heterozygous diploids from massively parallel shotgun sequencing data.
The latest version is 1.2.4.
To cite Platanus, please use the...
github.com - The automated reconstruction of genome sequences in ancient genome analysis is a multifaceted process.
EAGER encompasses both state-of-the-art tools for each step as well as new complementary tools tailored for ancient DNA data within a single...
novelseq.sourceforge.net - The NovelSeq framework is designed to detect novel sequence insertions using high throughput paired-end whole genome sequencing data.
http://novelseq.sourceforge.net/Home
Paper at https://www.ncbi.nlm.nih.gov/pubmed/20385726
www.animalgenome.org - The Blast Extension and Assembly Program (BEAP) is a computer program that uses a short starting DNA fragment, often a EST or partial gene segment, as "primer", to recursively blast nucleotide databases in an attempt to obtain all sequences that...
github.com - A JavaScript module for the visualization of genomic sequence graphs. It automatically generates a "tube map"-like visualization of sequence graphs which have been created with vg. (https://github.com/vgteam/vg)
Link to working demo:...
telatin.github.io - 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...
www.ncbi.nlm.nih.gov - Tbl2asn is a command-line program that automates the creation of sequence records for submission to GenBank. It uses many of the same functions as Sequin but is driven generally by data files. Tbl2asn generates .sqn files for submission to GenBank....
kallisto
Transcript abundance quantification from RNA-seq data (uses pseudoalignment for rapid determination of read compatibility with targets)
Software (C++)
https://pachterlab.github.io/kallisto/
Sailfish
Estimation of isoform abundances...