Webliography

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

..................Content has been hidden....................

You can't read the all page of ebook, please click here login for view all page.
Reset
13.59.156.15