Address of the bookmark: https://portal.nersc.gov/genomad

Address of the bookmark: https://github.com/andrewgull/MGERT

We have developed panHiTE, a comprehensive and accurate pipeline for TE detection in large-scale population genomes. It has been successfully applied to hundreds of plant population genomes, demonstrating its effectiveness and scalability.

For detailed instructions, please refer to the panHiTE tutorial.

Address of the bookmark: https://github.com/CSU-KangHu/HiTE

Prokka – Standalone command line tool, takes just a few minutes per genome. This is the best way to get good quality annotation in a flash, which is particularly useful if you have loads of genomes or need to annotate a pangenome or metagenome. Note however that the quality of functional information is not as good as RAST, and you will need several extra steps if you want to do functional profiling and pathway analysis of your genome(s)… which is in-built in RAST.

NCBI Prokaryotic Genome Annotation Pipeline is designed to annotate bacterial and archaeal genomes (chromosomes and plasmids).

Genome annotation is a multi-level process that includes prediction of protein-coding genes, as well as other functional genome units such as structural RNAs, tRNAs, small RNAs, pseudogenes, control regions, direct and inverted repeats, insertion sequences, transposons and other mobile elements.

PGAP: NCBI has developed an automatic prokaryotic genome annotation pipeline that combines ab initio gene prediction algorithms with homology based methods. The first version of NCBI Prokaryotic Genome Automatic Annotation Pipeline (PGAAP; see Pubmed Article) developed in 2005 has been replaced with an upgraded version that is capable of processing a larger data volume.  NCBI's annotation pipeline depends on several internal databases and is not currently available for download or use outside of the NCBI environment.

BEACON (automated tool for Bacterial GEnome Annotation ComparisON), a fast tool for an automated and a systematic comparison of different annotations of single genomes. The extended annotation assigns putative functions to many genes with unknown functions. BEACON is available under GNU General Public License version 3.0 and is accessible at: http://www.cbrc.kaust.edu.sa/BEACON/.

BlastKOLA: Assigns K numbers to the user's sequence data by BLAST searches, respectively, against a nonredundant set of KEGG GENES. KOALA (KEGG Orthology And Links Annotation) is KEGG's internal annotation tool for K number assignment of KEGG GENES using SSEARCH computation. Annotate Sequence in KEGG Mapper and Pathogen Checker in KEGG Pathogen are special interfaces to this server and can be executed in an interactive mode. BlastKOALA is suitable for annotating fully sequenced genomes.

PAGIT: Provides a toolkit for improving the quality of genome assemblies created via an assembly software. PAGIT compiled four tools: (i) ABACAS which classifies and orientates contigs and estimates the sizes of gaps between them; (ii) IMAGE uses paired-end reads to extend contigs and close gaps within the scaffolds; (iii) ICORN for identifying and correcting small errors in consensus sequences and; (iv) RATT for help annotation. The software was mainly created to analyze parasite genomes of up to about 300 Mb.

MAKER: A portable and easily configurable genome annotation pipeline. MAKER allows smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases. It identifies repeats, aligns ESTs and proteins to a genome, produces ab-initio gene predictions and automatically synthesizes these data into gene annotations having evidence-based quality values. MAKER's inputs are minimal and its ouputs can be directly loaded into a Generic Model Organism Database (GMOD). They can also be viewed in the Apollo genome browser; this feature of MAKER provides an easy means to annotate, view and edit individual contigs and BACs without the overhead of a database. MAKER is available for download and can be tested online via the MAKER Web Annotation Service (MWAS).

MyPro is a software pipeline for high-quality prokaryotic genome assembly and annotation. It was validated on 18 oral streptococcal strains to produce submission-ready, annotated draft genomes. MyPro installed as a virtual machine and supported by updated databases will enable biologists to perform quality prokaryotic genome assembly and annotation with ease.

Targeted bait capture is a technique for sequencing many loci simultaneously based on bait sequences. HybPiper pipeline starts with high-throughput sequencing reads (for example from Illumina MiSeq), and assigns them to target genes using BLASTx or BWA. The reads are distributed to separate directories, where they are assembled separately using SPAdes. The main output is a FASTA file of the (in frame) CDS portion of the sample for each target region, and a separate file with the translated protein sequence.

HybPiper also includes post-processing scripts, run after the main pipeline, to also extract the intronic regions flanking each exon, investigate putative paralogs, and calculate sequencing depth. For more information, please see our wiki.

HybPiper is run separately for each sample (single or paired-end sequence reads). When HybPiper generates sequence files from the reads, it does so in a standardized directory hierarchy. Many of the post-processing scripts rely on this directory hierarchy, so do not modify it after running the initial pipeline. It is a good idea to run the pipeline for each sample from the same directory. You will end up with one directory per run of HybPiper, and some of the later scripts take advantage of this predictable directory structure.

Address of the bookmark: https://github.com/mossmatters/HybPiper

Key Findings of the Study:

1. Alu Insertion and Tail Loss:
   The researchers discovered an Alu-mediated genetic change in a common ancestor of modern apes and humans. This change disrupted the normal function of a gene involved in tail development, leading to the suppression of tail formation.

2. Gene Disruption Mechanism:
   The Alu insertion was found within a regulatory region of the TBXT gene (also known as T or Brachyury), which is crucial for tail development in vertebrates. This insertion likely altered the gene's expression patterns, leading to tail reduction over evolutionary time.

3. Functional Evidence from Model Organisms:
   To test their hypothesis, the researchers introduced similar genetic modifications in mice. The modified mice exhibited shortened or absent tails, supporting the idea that the identified mutation played a role in tail loss in hominoids.

4. Evolutionary Implications:
   The findings suggest that small, random genomic changes—such as transposable element insertions—can have profound effects on body morphology. This study provides evidence that mobile DNA elements (like Alu) can drive major evolutionary transitions.

5. Relevance to Human Evolution:
   Understanding the genetic basis of tail loss helps in reconstructing the evolutionary history of hominins (the lineage that includes humans and our extinct relatives). It also sheds light on how genetic variations contribute to anatomical diversity among primates.

Significance of the Study:

This research highlights the role of transposable elements in shaping evolutionary traits and provides a concrete genetic explanation for a defining characteristic of humans and great apes. It also demonstrates how mutations in regulatory regions of developmental genes can lead to significant anatomical changes.

Address of the bookmark: https://github.com/reubwn/hgt

Address of the bookmark: https://github.com/Magdoll/Cogent

ftp://ftp.ncbi.nih.gov/genomes/

https://hgdownload.soe.ucsc.edu/downloads.html

Address of the bookmark: ftp://ftp.ncbi.nih.gov/genomes/