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Bioinformatics Scripts & Commands
Python Install Python Windows: https://www.python.org/downloads/windows/ (Don’t forget to tick PATH in first step of installation) Install Virtual Environment Windows: Virtual Environment Creation Windows: Go to the desired folder and open command prompt/terminal/powershell in this folder by pressing “shift” key and “right click” in mouse then select “terminal” or “powershell” . Then type following commands Activate/Use…
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Bioinformatics Tools
Sequence Analysis Tools Pairwise Sequence Alignment Tools Basic Local Alignment Search Tool (BLAST) : https://blast.ncbi.nlm.nih.gov/Blast.cgi (Alignment and Similarity Searching) Multiple Sequence Alignment Tools Clustal Omega: https://www.ebi.ac.uk/jdispatcher/msa/clustalo Clustal W: https://www.genome.jp/tools-bin/clustalw MAFFT : https://mafft.cbrc.jp/alignment/software/ Sequence Analysis Tools Ensemble: https://asia.ensembl.org/index.html (Exon, Intron, Genomic Content) UniProt: https://www.uniprot.org/ (Functional domains, variants, PTMs) Motif Based Sequence Analysis Tool MEME : https://meme-suite.org/meme/…
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Basic Linux(Debian) Command
Full Forms sudo: super user do apt: Advanced Packaging Tool pip: Package Installer for Python dpkg: Debian PacKaGe manager Press Ctrl + O for Save clear: Clean terminal sudo shutdown now : Shut Down Lubuntu ssh linux default port: port: 22 Type Linux Command Function Update sudo apt update sudo apt upgrade …
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Genetic Code
Defination : It is the set of rules by which the information encoded in the nucleotide sequence of mRNA is translated into the amino acid sequence of protein. Central Dogma: The theory that states unidirectional flow of genetic information i.e; DNA to RNA to Protein DNA to DNA ( Replication), DNA to RNA (Transcription), RNA…
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Types and Lists of Bioinformatics Databases
Bioinformatics Databases Human Genomic Browser NCBI : https://www.ncbi.nlm.nih.gov/gdv/ UCSC: https://genome-asia.ucsc.edu/ Sequence Database (Nucleotide or Amino Acid Sequence) : Main Domain GenBank https://www.ncbi.nlm.nih.gov/ (All Databases, Primary Database) Ensembl https://www.ensembl.org/ (Nucleotide sequences) DDBJ https://www.ddbj.nig.ac.jp/ (Nucleotide sequences, Primary Database) EMBL-EBI https://www.ebi.ac.uk/ (Nucleotide sequences, Primary Database) UniProt https://www.uniprot.org/ (Amino Acid Sequence, Secondary Database) BV-BRC https://www.bv-brc.org/ (Bacterial and Viral Bioinformatics…