Biological data formats supported by Biopython, including FASTA, FASTQ, GenBank, SAM/BAM & PDB with examples. Reading and Writing Biological Data formats with SeqIO module.
Sequence Read Archive (SRA) data is the largest publicly available repository of high throughput sequencing data; available through multiple cloud providers and NCBI servers
Primer3Plus is an advanced web interface for PCR primer design, offering intuitive controls and automated features for cloning, sequencing, and custom primer design.
SPAdes is a comprehensive genome assembly toolkit that processes both short-read (Illumina, IonTorrent) and hybrid long-read (PacBio, Oxford Nanopore) sequencing data.
Adenovirus contains a 36-Kb linear dsDNA genome with ITRs at both ends and consists of early (E1-4) and late (L1-5) heavily spliced transcripts. Of the 57 known human adenovirus types, Ad5 is most commonly used for vectors, utilizing CAR for cell entry.
Pichia pastoris has many of the advantages of higher eukaryotic expression systems such as protein processing, protein folding, and the availability of posttranslational modifications, while being as easy to manipulate as E. coli or Saccharomyces cerevisiae. It is faster, easier, and less expensive to use than other eukaryotic expression systems and generally gives higher expression levels
pBR322 is a circular, double-stranded DNA plasmid, 4 361 base pairs that contains important features such as antibiotic resistance genes for ampicillin (AmpR) and tetracycline (TetR), as well as multiple restriction sites ((at least 40, restriction sites (EcoR1, HindIII, Pst1), making it a versatile tool for cloning and gene expression studies.
Lambda EMBL3 and EMBL4 are high-capacity vectors derived from bacteriophage lambda, used for genomic library construction. They utilize the Spi- phenotype selection method, which allows recombinant phages to grow on P2 lysogenic strains by replacing stuffer DNA with inserts.
The baculovirus, Autographa Californica (the alfalfa looper) multiple nuclear polyhedrosis virus (AcMNPV) has been used extensively as an expression vector using a genetically engineered cell…
Introduction to BLAST BLAST stands for Basic Local Alignment Search Tool (BLAST). It is an algorithm for comparing primary biological sequence information, such as amino…
Introduction Epigenetic modifications, which involve changes to the genome without altering the DNA sequence, play a crucial role in regulating gene expression. These modifications include…
The genetic code is composed of nucleotide triplets code in which each codon in an mRNA specifies one amino acid. Genetic code was cracked by the combined efforts of Marshall Nirenberg, Severo Ochoa, H. Ghobind Khorana, Philip Leder, and their colleagues who worked out the meaning of all 64 triplet codons.
The Wobble Hypothesis, proposed by Francis Crick in 1966, explains the degeneracy of the genetic code. The hypothesis attributes this degeneracy to imprecise pairing between the…
The collaboration between OpenAI and Retro Biosciences introduces a generative model that redesigns Yamanaka reprogramming factors to dramatically improve reprogramming efficiency. This development signals a…
OpenAI and Retro Biosciences used AI to design proteins that boost stem-cell reprogramming over 50X, showing how machine learning can accelerate regenerative medicine and create biological tools beyond what nature provides.
The SRA Toolkit provides two essential tools for downloading and extracting sequencing data: 1. prefetch: Downloads SRA files locally for faster processing. 2. fasterq-dump: Converts SRA files to FASTQ format
The Yeast Two-Hybrid (Y2H) system or Yeast Two-Hybrid Assay represents a powerful in vivo technique for detecting and analyzing protein-protein interactions, where the physical association between bait and prey proteins triggers transcriptional activation of reporter genes in yeast cells.
Ligase chain reaction (LCR) is a thermostable DNA ligase-dependent DNA amplification which can be initiated by repetitive cycles of the ligation of adjacent hybridized DNA probes for the achievement of exponential amplification of target DNA
Bacterial artificial chromosomes (BACs) are single-copy-number, high-capacity circular DNA vectors derived from Escherichia coli fertility factor (F-plasmids); they can accommodate approximately 350 kb of inserted DNA.
Using Jupyter Notebook, a versatile tool for data analysis, visualization, and interactive programming, can streamline running Biopython code for bioinformatics tasks.
Sanger sequencing relies on electrophoresis and involves the random incorporation of chain-terminating dideoxynucleotides by DNA polymerase during in vitro DNA replication
A Yeast Artificial Chromosome (YAC) is a shuttle high-capacity useful for the physical mapping of complex genomes and for the cloning of large genes. It mimics a natural chromosome in yeast cells and includes essential elements such as an ARS1, a CEN4, and TEL, and selectable markers (ura3, trp1, and his3)