Bioinformatics Cheat Sheet: A Step-by-Step Guide for Beginners

This cheat sheet is designed to help bioinformaticians, especially beginners, quickly reference key concepts, commands, scripts, and useful tools that are essential in bioinformatics workflows. It includes basic Unix commands, Perl one-liners, Python snippets, and helpful biological concepts that every bioinformatician should be familiar with.

1. Key Biological Concepts and Units

• IUPAC Ambiguity Codes for Nucleotides
  • A = Adenine
  • C = Cytosine
  • G = Guanine
  • T = Thymine
  • U = Uracil (RNA only)
  • R = A or G (Purines)
  • Y = C or T (Pyrimidines)
  • M = A or C
  • K = G or T
  • S = G or C
  • W = A or T
  • B = C, G, or T
  • D = A, G, or T
  • H = A, C, or T
  • V = A, C, or G
  • N = Any base
• Amino Acid Single-Letter Codes
  • A = Alanine
  • C = Cysteine
  • D = Aspartic Acid
  • E = Glutamic Acid
  • F = Phenylalanine
  • G = Glycine
  • H = Histidine
  • I = Isoleucine
  • K = Lysine
  • L = Leucine
  • M = Methionine
  • N = Asparagine
  • P = Proline
  • Q = Glutamine
  • R = Arginine
  • S = Serine
  • T = Threonine
  • V = Valine
  • W = Tryptophan
  • Y = Tyrosine
• 1 Human Genome ≈ 7 pg of DNA
  • This is useful for DNA quantification.
• 1 Base Pair (bp) = 660 Daltons
  • This conversion is helpful when calculating the molecular weight of DNA sequences.

2. Unix Commands and One-Liners

• Convert Unix to Windows Line Endings
  bash

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  sed -i 's/$/\r/' file.txt

• Sort a BED File by Chromosome and Position
  bash

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  sort -k1,1 -k2,2n file.bed > file.sorted.bed

• Find and Replace in Multiple Files
  bash

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  perl -pi -w -e 's/old_value/new_value/g' *.txt

• Remove Header from a File
  bash

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  tail -n +2 file.txt > file_no_header.txt

• Sum the Values in the First Column of a File
  bash

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  awk '{s+=$1} END {print s}' file.txt

• Print a Specific Line from a File (e.g., Line 83)
  bash

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  sed -n '83p' file.txt

• Insert a Header Line into a File
  bash

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  sed -i '1i# New header line' file.txt


3. Perl One-Liners

• Remove Windows Line Breaks (convert to Unix format)
  bash

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  perl -pi -e 's/\r\n/\n/g' file.txt

• Replace String in Multiple Files
  bash

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  perl -pi -e 's/old_string/new_string/g' *.txt

• Simple Text Processing with Perl
  bash

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  perl -ne 'print if /pattern/' file.txt

• Count the Number of Lines in a File
  bash

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  perl -lne 'END { print $. }' file.txt


4. Python Scripts for Bioinformatics

• Calculate GC Content of a DNA Sequence
  python

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  def gc_content(sequence):
gc_count = sequence.count('G') + sequence.count('C')
return (gc_count / len(sequence)) * 100

• Read and Parse a FASTA File
  python

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  def read_fasta(file):
with open(file, 'r') as f:
sequences = {}
seq_name = ''
seq_data = ''
for line in f:
if line.startswith('>'):
if seq_name:
sequences[seq_name] = seq_data
seq_name = line[1:].strip()
seq_data = ''
else:
seq_data += line.strip()
sequences[seq_name] = seq_data
return sequences

• Basic Sequence Alignment Using Biopython
  python

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  from Bio import pairwise2
  from Bio.pairwise2 import format_alignment

  seq1 = "AGCTGTA"
seq2 = "AGCTGCA"
alignments = pairwise2.align.globalxx(seq1, seq2)
for alignment in alignments:
print(format_alignment(*alignment))


5. Handy Biological Conversion Factors

• Molecular Weights
  • 1 mole of DNA = 6.022 × 10²³ molecules (Avogadro’s number)
  • 1 bp = 660 Daltons (molecular weight of a base pair)
• Volume Conversions
  • 1 mm³ = 1 µL
  • 1 µm³ = 1 pL
  • 1 liter = 1000 mL

6. Tm Calculation for DNA Sequences

• Tm (Melting Temperature) Estimation Using GC Content
  For a rough estimate, use the formula:
  Tm = 2°C × (A + T) + 4°C × (G + C)
  Where A, T, G, and C are the count of the respective bases in the sequence.

7. Bioinformatics Tools and References

• BLAST (Basic Local Alignment Search Tool)
  • Used for comparing nucleotide or protein sequences to databases.
• Bowtie/Tophat
  • Aligns short reads to a reference genome.
  • Bowtie: for large-scale alignment.
  • Tophat: for RNA-Seq data analysis.
• Samtools
  • Handles the SAM/BAM format for sequencing data.
  • Example command to view a BAM file:
    bash

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    samtools view file.bam

• BEDTools
  • A suite of tools for manipulating genomic intervals.
  • Example: to merge overlapping regions in a BED file:
    bash

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    bedtools merge -i file.bed > merged.bed


8. Best Practices and Tips

• Version Control: Always use version control (e.g., Git) for your bioinformatics projects.
• Document Your Code: Add comments to scripts and notebooks to ensure reproducibility.
• Reproducibility: Use virtual environments (e.g., Conda or Docker) to ensure reproducibility across systems.
• Data Formats: Understand the file formats you are working with (e.g., FASTA, FASTQ, BAM, VCF).
• Efficient Data Processing: Use parallel processing and optimize algorithms for large datasets (e.g., RNA-Seq).

Conclusion

This Bioinformatics Cheat Sheet offers a collection of essential commands, conversions, and tools for bioinformaticians. As you progress in bioinformatics, adapting these tools to your specific research needs and automating repetitive tasks will make your work more efficient. Keep this sheet handy as a quick reference to streamline your bioinformatics workflows.