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

The Ensembl comparative genomics resources are one such reference set that facilitates comprehensive and reproducible analysis of chordate genome data. Ensembl computes pairwise and multiple whole-genome alignments from which large-scale synteny, per-base conservation scores and constrained elements are obtained. Gene alignments are used to define Ensembl Protein Families, GeneTrees and homologies for both protein-coding and non-coding RNA genes. These resources are updated frequently and have a consistent informatics infrastructure and data presentation across all supported species. Specialized web-based visualizations are also available including synteny displays, collapsible gene tree plots, a gene family locator and different alignment views. The Ensembl comparative genomics infrastructure is extensively reused for the analysis of non-vertebrate species by other projects including Ensembl Genomes and Gramene and much of the information here is relevant to these projects. The consistency of the annotation across species and the focus on vertebrates makes Ensembl an ideal system to perform and support vertebrate comparative genomic analyses. We use robust software and pipelines to produce reference comparative data and make it freely available.

Database URL: http://www.ensembl.org.

Address of the bookmark: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4761110/

Compare structural and functional annotations of proteins between sequenced genomes.

Following are the list of resource and location for TE discovery and TE detection:

BLASTER suite http://urgi.versailles.inra.fr/development/blaster/ 

Censor http://www.girinst.org/censor/download.php 

find_ltr http://darwin.informatics.indiana.edu/cgi-bin/evolution/ltr.pl 

FINDMITE http://jaketu.biochem.vt.edu/dl_software.htm

HMMER http://hmmer.janelia.org/

LTR_FINDER http://tlife.fudan.edu.cn/ltr_finder/

LTR_STRUC http://www.genetics.uga.edu/retrolab/data/LTR_Struc.html

LTR_MINER http://genomebiology.com/2004/5/10/R79/suppl/s7

LTR_par http://www.eecs.wsu.edu/~ananth/software.htm

MAK http://wesslercluster.plantbio.uga.edu/mak06.html

MaskerAid http://blast.wustl.edu/maskeraid/

mer-engine http://mer-engine.cshl.edu/mer-home.php

mreps http://bioinfo.lifl.fr/mreps/

PILER http://www.drive5.com/piler/

PLOTREP http://repeats.abc.hu/cgi-bin/plotrep.pl

RepBase http://www.girinst.org/

RepeatFinder http://cbcb.umd.edu/software/RepeatFinder/

RepeatGluer http://nbcr.sdsc.edu/euler/intro_tmp.htm

RepeatMasker http://www.repeatmasker.org/

RepeatRunner http://www.yandell-lab.org/repeat_runner/index.html

RepeatScout http://repeatscout.bioprojects.org/

repeat-match http://mummer.sourceforge.net/

REPuter http://www.genomes.de/

RetroMap http://www.burchsite.com/bioi/RetroMapHome.html

SMaRTFinder http://bioinf.dimi.uniud.it/software/software/smartfinder

Tandem Repeats Finder http://tandem.bu.edu/trf/trf.html

Transposon Cluster Finder http://www.mssm.edu/labs/warbup01/paper/files.html

TE nest http://www.plantgdb.org/prj/TE_nest/TE_nest.html

TRANSPO http://alggen.lsi.upc.es/recerca/search/transpo/transpo.html

TSDfinder http://www.ncbi.nlm.nih.gov/CBBresearch/Landsman/TSDfinder/

Tu Lab TE tools http://jaketu.biochem.vt.edu/dl_software.htm

WU-BLAST http://blast.wustl.edu

DrugBank:

a bioinformatics- cheminformatics resource combining detailed drug data with comprehensive drug target information with >4900 drug (~3500 experimental) and >1500 non-redundant protein entries http://www.drugbank.ca/

Drug-Target Network:

network data of 890 drugs and 394 target human proteins http://www.nature.com/nbt/journal/v25/ n10/suppinfo/nbt1338_S1.html

Drug-Therapy Network:

three layers of drug-therapy networks according to the ATC classification http://www.biomedcentral.com/1471-2210/8/5/additional/

FDA Orange Book:

approved drug products with therapeutic equivalence evaluations http://www.fda.gov/cder/ob/HIDdb: Thomson Investigational drugs database including information on 107000 patents, 25000 investigational drugs and 80000 chemical structures http://scientific.thomson.com/products/iddb/HOMIM: a knowledgebase of human genes and genetic disorders http://www.ncbi.nlm.nih.gov/ sites/entrez?db=omim

PDTD:

3D drug target structure database with a target identification option http://www.dddc.ac.cn/pdtd/

Predicted drug targets:

a set of 1383 predicted drug targets http://www.biomedcentral.com/1471-2105/8/353/additional/ [25] Protein ligand network: a network of 4208 ligands and ~15000 binding sites http://pbil.kaist.ac.kr/~parkkw/Lnet/

TDR Targets Database:

identification and ranking targets against neglected tropical diseases http://tdrtargets.org/

Therapeutic Target Database:

lists >1500 therapeutic targets, disease conditions and corresponding drugs http://xin.cz3.nus.edu.sg/group/cjttd/ttd.asp

Desirable : Research or teaching experience in Bioinformatics and Computational Biology.
Honorarium : Rs. 1,000/- per lecture (subject to a maximum of 25,000/- per month)
How to apply

Interested eligible candidates may attend the 'walk-in' interview along with all original certificates and testimonials with a copy of their bio-data. Walk-in-interview will be held on 28.09.2015 (Monday), 03:00 P.M. at the office of the Dean, School of Life Sciences, Science Block — I, Pondicherry University, Puducherry — 605 014. Candidates reporting after 03:00 P.M. will not be entertained.

More at http://www.pondiuni.edu.in/news/walk-interview-guest-faculty-centre-bioinformatics