bioinformaticssoftwareandtools.co.in/bio_tools.php#restriction_table – acquires various online bioinformatics databases and tools

ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF_000298735.2_Oar_v4.0/GCF_000298735.2_Oar_v4.0_rna.fna.gz

ftp://ftp.ncbi.nlm.nih.gov/pub/factsheets/HowTo_BLASTGuide.pdf – an enhanced report for search results generated by the BLAST web service

http://align.bmr.kyushu‐u.ac.jp/mafft/software/ – another efficient MSA tool

http://biit.cs.ut.ee/gprofiler/ – web server link for characterizing and manipulating gene lists of high‐throughput genomics

http://bioinf.cs.ucl.ac.uk/psipred/ – protein sequence analysis tool

http://bioinfogp.cnb.csic.es/tools/venny/ – tool for comparing lists with Venn Diagrams

http://biology.unm.edu/ccouncil/Biology_203/Summaries/Phylogeny.htm

http://blast.ncbi.nlm.nih.gov/Blast.cgi – Blast home page

http://catchenlab.life.illinois.edu/stacks/comp/denovo_map.php – the software pipeline “Stack” provides the scripts for necessary analysis of SNP mining

http://creskolab.uoregon.edu/stacks/ – software pipeline for building loci from short‐read sequences

http://dnafsminer.bic.nus.edu.sg/Tis.html – link is used to predict translation initiation site(s) in vertebrate DNA/mRNA/cDNA sequences

http://emboss.sourceforge.net/docs/themes/SequenceFormats.html – an online sequence format conversion tool (along with an explanation of the basic features of sequence format conversion)

http://en.bio‐soft.net/format/MACAW.html – link to Multiple Alignment Construction & Analysis Workbench (MACAW) software

http://espressosoftware.com/pages/sputnik.jsp

http://eu.idtdna.com/site – home page of integrated DNA technologies

http://eu.idtdna.com/UNAFold? – site contains information regarding various components (Resuspension Calculator; Dilution Calculator; qPCR Assay Design) of UNAFold Tool

http://evolution.berkeley.edu/evolibrary/glossary/glossary_popup.php?word=outgroup – information about glossary of evolution of origin of life

http://exon.gatech.edu/gmhmmp.cgi – provides access to gene prediction program GeneMark.hmm prokaryotic (versions 3.25)

http://genes.mit.edu/GENSCAN.html – link provides access to the program GenScan for predicting the locations and exon‐intron structure of genes in genomic sequences fron a variety of organisms

http://genome.crg.es/courses/Bioinformatics2003_genefinding/results/GENSCAN.html – explanation on GENSCAN output is available

http://genome.crg.es/courses/Bioinformatics2003_promoters/ – Online tutorial, “Regulation of Human obese protein geneRegulation of Human obese protein gene”, which demonstrates the exercise on transcription binding site prediction

http://gor.bb.iastate.edu/ – tool for predicting secondary structure of proteins

http://lion.img.cas.cz/sms2/index.html/ – site contains a program suit for manipulating DNA and Protein sequences

http://molprobity.biochem.duke.edu/ – home page of molprobity

http://mordred.bioc.cam.ac.uk/~rapper/rampage.php – site used for Ramachandran plot analysis

http://myhits.isb‐sib.ch/util/dotlet/doc/dotlet_about.html – Dotlet is online software used for diagonal plotting of sequences.

http://opal.biology.gatech.edu/GeneMark/ – online gene prediction programme

http://petang.cgu.edu.tw/Bioinfomatics/Lecture/0_HTS/04/20120316.pdf – guidelines for using miRDeep2

http://pgrc.ipkgatersleben.de/misa/ – a microsatellite identification tool

http://pgrc.ipk‐gatersleben.de/misa/misa.html – a microsatellite identification tool

http://plantgrn.noble.org/psRNATarget/ – a Plant Small RNA Target Analysis tool

http://primer3.ut.ee/ – site used to screen candidate oligos against mispriming library

http://raptorx.uchicago.edu/StructurePrediction/predict/ – online protein sequence prediction (up to 20 proteins) tool

http://self.gutenberg.org/articles/Long_branch_attraction

http://sonnhammer.sbc.su.se/Dotter.html – Dotter is a graphical dotplot program for thorough comparison of two molecular sequences

http://swift.cmbi.ru.nl/servers/html/index.html – an online algorithm used to calculate data from symmetry, torsion angles, polar fraction through protein analysis and bond angles

http://swissmodel.expasy.org/workspace/index.php?func=show_workspace – an online analysis for SWISS‐MODEL workspace

http://tandem.bu.edu/trf/trf.html – public database of tandem repeats for users to run their own sequences

http://targetscan.org/ – site belonging to TargetScan, used to predict biological targets of miRNAs by searching for the presence of 8mer, 7mer, and 6mer sites

http://tools.neb.com/NEBcutter2/index.webline – tool for the identification of restriction enzyme sites.

http://www.acdlabs.com/resources/freeware/chemsketch/ – ACD/Chemsketch

http://www.biobase‐international.com/product/transcription‐factor‐binding‐sites – online MATCH Analysis tool to Predict binding sites for Transcription Factors in a particular DNA sequence

http://www.biochem.ucl.ac.uk/bsm/dbbrowser/CINEMA2.1/ – online multiple sequence alignment tool called Color INteractive Editor for Multiple Alignments (CINEMA)

http://www.bioinformatics.org/JaMBW/1/2/: a Java‐based online sequence format conversion tool

http://www.biomedcentral.com/content/supplementary/1471‐2164‐11‐156‐s2/Additionalfile2/Genscan_output/GENSCAN%20output%20EG926217.htm – sequence output tool

http://www.cambridgesoft.com/software/overview.aspx: ChemDraw – site for desktop and enterprise software

http://www.cbi.pku.edu.cn/docs/faq/blastspecifics.html – a useful page that has frequently asked questions (FAQs) on BLAST

http://www.cbs.dtu.dk/services/NetStart/ – online server to produce neutral network predictions of translation start in vertebrate and Arabidopsis thaliana nucleotide sequences

http://www.deduveinstitute.be/~opperd/private/upgma.html – online tree construction tool

http://www.ebi.ac.uk/Tools/clustalw2/index.html (Clustal W) – site for online multiple sequence alignment

http://www.ebi.ac.uk/Tools/dbfetch/dbfetch/dbfetch.databases – provides information on a large number of dbfetch databases

http://www.ebi.ac.uk/Tools/msa/clustalo/ – link for online multiple sequence alignment tool Clustal Omega

http://www.ebi.ac.uk/Tools/sfc/emboss_seqret/ – sequence format conversion tool provided by EBI.

http://www.ebi.ac.uk/Tools/webservices/ – provides programmatic access to various data resources and analysis tools EMBL‐EBI

http://www.es.embnet.org/Services/MolBio/t‐coffee/ – online T‐Coffee tool for MSA

http://www.gene‐regulation.com/cgi‐bin/pub/programs/match/bin/match.cgi – a site for Match tool that is used for in silico transcription factor binding studies

http://www.hhmi.umbc.edu/toolkit/ClustalWGuide.html – provides help and guidelines on Clustal W multiple sequence alignment program

http://www.hku.hk/bruhk/gcgdoc/dotplot.html – Dot‐plot(+) is used to identify the overlapping portions of two sequences and to identify the repeats and inverted repeats of a particular sequence.

http://www.jalview.org/ – link to Java Alignment Viewer (JALVIEW) that uses a Java‐based platform

http://www.kazusa.or.jp/codon/ – a codon usage database that holds records of thousands of organisms

http://www.life.umd.edu/classroom/bsci338m/Lectures/Systematics.html – provides information regarding importance of phylogenesis, biodiversity and evolution

http://www.life.umd.edu/classroom/bsci338m/Lectures/Systematics.html – provides information regarding importance of phylogenesis, biodiversity and evolution

http://www.megasoftware.net/ – an integrated tool for conducting automatic and manual sequence alignment

http://www.microrna.org – resource for miRNA target prediction and expression

http://www.ncbi.nlm.nih.gov/books/NBK153387/ – book source for blast sequence analysis tool

http://www.ncbi.nlm.nih.gov/protein/ – a protein database

http://www.ncbi.nlm.nih.gov/Structure/CN3D/cn3d.shtml – 3‐dimensional structure viewer tool

http://www.ncbi.nlm.nih.gov/tools/primer‐blast/index.cgi?LINK_LOC=BlastHome – primer designing too

http://www.ncbi.nlm.nih.gov/WebSub/?tool=genbank – site used for sequence submission

http://www.rcsb.org/pdb/ – Protein databank site

http://www.simsoup.info/Origin_Landmarks_Oparin_Haldane.html – webpage on Oparin‐Haldane hypothesis

http://www.uniprot.org/uniprot/ – provides the scientific community with a comprehensive, high‐quality and freely accessible resource of protein sequence and functional information

http://www.vcru.wisc.edu/simonlab/bioinformatics/programs/stacks/ref_map.pl.txt – explanation of the commands for Reference mapping (ref_map.pl), in Stacks pipeline

http://www.w3schools.com/html/html_intro.asp – a web developer’s site that has a discussion on HTML documentation

http://www‐bimas.cit.nih.gov/molbio/readseq/ – ReadSeq is an online sequence format conversion tool

http://zinc.docking.org/: ZINC – database used for virtual screening of commercially available compounds

https://david.ncifcrf.gov – link provides information regarding a comprehensive set of functional annotation tools for investigators to understand biological meaning behind large list of genes

https://eu.idtdna.com/analyzer/Applications/OligoAnalyzer/ – site used to examine an oligonucleotide for primer‐dimer, self‐ dimer, hetero‐dimer etc.

https://genome.ucsc.edu – site contains the reference sequence and working draft assemblies for a large collection of genomes

https://pubchem.ncbi.nlm.nih.gov/ – provides information on the biological activities of small molecules

https://software.broadinstitute.org/gatk/download/ – to download the latest version of GATK

https://sourceforge.net/projects/bowtie‐bio/files/bowtie/1.1.1/ – a very fast short‐read aligner for DNA‐seq or RNA‐seq studies

https://www.broadinstitute.org/gatk/index.php

https://www.cgl.ucsf.edu/chimera/ – program used for interactive visualization and analysis of molecular structures and related data

https://www.mdc‐berlin.de/36105849/en/research/research_teams/systems_biology_of_gene_regulatory_elements/projects/miRDeep/documentation – miRDeep commands and explanation

rasmol.org/ – RasMol is a program for molecular graphics visualization

wssp.rutgers.edu/StudentScholars/WSSP08/DotPlotter/DotPlotPractice.html – site for dotplot analysis of amino acid and nucleic acid sequences. This site is not functional currently.

ww2.chemistry.gatech.edu/~williams/bCourse_Information/4581/labs/tbp/rasmol/rasmol_tbp_fset.html – site for RasMol tutorial

www.bioinformatics.org/sms2/mirror.html/ – site for online databases and bioinformatics tools for analysis.

www.computerhope.com/jargon – a dictionary and glossary for computer terms

www.expasy.org/ – maintains biological databases and online tools related to proteomics, genomics, phylogenetics, etc.

www.ncbi.nlm.nih.gov/nucleotide/ – very useful and popular primary repository of nucleotide sequences.

www.rcsb.org/pdb/home/home.do – database for biomacromolecular structures.

www.repeatmasker.org/ – program used to screen DNA sequences for interspersed repeats and low complexity

www.swissdock.ch/docking: SwissDock server – used to search target proteins or ligand

www.vivo.colostate.edu/molkit/dnadot/ – site for nucleic acid dot plot. Currently not available