bioinformatics 1

Bioinformatics

Combines biology with computing statistics and data analysis to interpret biological information such as DNA RNA and protein sequences.

Genomics

Study of complete genomes and genome-scale data including structure variation function and evolution.

Genetics

Study often focused on individual genes traits and inheritance rather than entire genomes.

Sequence alignment

Comparison of biological sequences to identify matching positions differences conserved regions insertions and deletions.

Database searching

Comparing a biological sequence against stored sequences to find related sequences.

Genome assembly

Computational reconstruction of longer genomic sequences from sequencing data.

Gene prediction

Identifying likely gene locations in DNA sequence data.

Annotation

Adding biological information such as identity or function to sequence data.

Gene-expression analysis

Studying patterns in how genes are expressed.

Metagenomics

Analysis of genetic material from communities of organisms.

Comparative genomics

Comparison of genomes to study similarities differences and evolution.

Python

Readable programming language useful for scripting automation data analysis machine learning and rapid development.

C

Compiled language useful for fast memory-efficient processing of very large sequence datasets.

C++

High-performance language with features for developing larger software tools.

R

Language widely used for statistics visualization and biological data analysis.

Perl

Language historically important for biological sequence and text processing.

Bash

Language for automating Unix commands and command-line pipelines.

Why C can be faster than Python

C compiles to machine code and allows direct control over memory and data structures.

Why Python is popular

Python programs are often faster to write and easier to read and benefit from many scientific libraries.

Global alignment

Aligns the full lengths of two sequences.

Local alignment

Finds the best matching region within two sequences.

Needle

Program for global alignment using the Needleman-Wunsch algorithm.

Water

Program for local alignment using the Smith-Waterman algorithm.

Needleman-Wunsch

Classic algorithm used for global sequence alignment.

Smith-Waterman

Classic algorithm used for local sequence alignment.

When to use Needle

When most of both sequences are expected to be related such as similar-length homologous sequences.

When to use Water

When only part of the sequences may be related such as a shared protein domain.

Conserved position

Sequence position that remains similar across compared sequences.

Insertion or deletion

Gain or loss of sequence residues that may appear as gaps in an alignment.

Substitution matrix

Table of scores for amino acid matches and replacements based on observed substitution patterns.

PAM

Point Accepted Mutation matrix based on accepted substitutions in closely related proteins.

PAM1

Matrix representing a very small evolutionary distance.

Higher PAM number

Indicates greater evolutionary distance.

BLOSUM

BLOcks SUbstitution Matrix constructed from conserved blocks of protein families.

BLOSUM62

Common general-purpose amino acid substitution matrix.

Lower BLOSUM number

Used for more divergent protein sequences.

Positive substitution score

Substitution occurs more often than expected by chance and may reflect a conservative change.

Zero substitution score

Substitution occurs about as often as expected by chance.

Negative substitution score

Substitution occurs less often than expected by chance.

Dot plot

Visual comparison of two sequences with a dot where positions match.

Long diagonal on a dot plot

Indicates strong sequence similarity.

Break in dot plot diagonal

May indicate an insertion or deletion.

Parallel dot plot diagonals

May indicate repeated or duplicated regions.

Reverse diagonal on a dot plot

May indicate an inversion.

BLAST

Basic Local Alignment Search Tool that rapidly searches sequence databases for local similarity to a query.

Heuristic search

Fast search approach used by BLAST to make large database searches practical.

Query sequence

Sequence submitted for comparison against a database.

blastn

Compares a nucleotide query with a nucleotide database.

blastp

Compares a protein query with a protein database.

blastx

Translates a nucleotide query and searches a protein database.

tblastn

Compares a protein query with a translated nucleotide database.

tblastx

Compares translated nucleotide queries with translated nucleotide database sequences.

Percent identity

Percentage of aligned positions with exactly matching residues.

Query coverage

Portion of the query sequence included in an alignment.

Bit score

Normalized alignment score where higher values indicate a better-scoring match.

E-value

Expected number of matches with the observed score or better that could occur by chance.

Low E-value

Indicates a more statistically significant BLAST match.

BLASTP middle-line amino acid letter

Indicates an exact amino acid match.

BLASTP middle-line plus sign

Indicates a conservative substitution with a positive score.

BLASTP middle-line blank

Indicates a mismatch.

BLASTP alignment dash

Indicates a gap.

Unix

Operating system environment commonly used to run command-line bioinformatics tools.

pwd

Prints the current working directory.

ls

Lists files and directories.

cd

Changes the current directory.

mkdir

Creates a new directory.

cp

Copies a file.

mv

Moves or renames a file.

rm

Removes a file.

cat

Displays file contents.

less

Opens a file for scrolling through its contents.

head

Displays the beginning of a file.

tail

Displays the end of a file.

grep

Searches text for a specified pattern.

wc -l

Counts lines in a file or input.

curl

Retrieves data from a URL.

tar

Creates or extracts archive files.

FASTA file

Text-based biological sequence format in which each sequence has a header beginning with >.

FASTA header

Line beginning with > that identifies a sequence record.

grep -c "^>" sequences.fasta

Counts FASTA sequence headers and therefore the number of sequences in the file.

Unix >

Redirects output into a file and overwrites its existing contents.

Unix >>

Appends output to the end of a file.

Unix pipe |

Passes the output of one command as input to another command.

grep "^>" sequences.fasta | wc -l

Counts FASTA headers by piping matching lines to a line-count command.

tar -xvf files.tar

Extracts an uncompressed tar archive.

tar -cvf files.tar folder/

Creates an uncompressed tar archive from a folder.

tar -xzvf files.tar.gz

Extracts a gzip-compressed tar archive.

tar -czvf files.tar.gz folder/

Creates a gzip-compressed tar archive.

SeqKit

Command-line toolkit for summarizing manipulating and analyzing FASTA and FASTQ files.

seqkit stats

Displays sequence counts and length statistics.

seqkit grep

Finds or extracts matching sequence records.

seqkit subseq

Extracts a specified region of a sequence.

seqkit sort -l

Sorts sequences by length.

seqkit fx2tab -n -g

Displays each sequence name and its GC content.

GC content

Proportion of bases in a sequence that are guanine or cytosine.

Reverse complement

Nucleotide sequence made by reversing the order and replacing each base with its complementary base.

UniProt

Protein sequence and function database with annotations names and cross-references.

PDB

Protein Data Bank containing experimentally determined three-dimensional structures of biological macromolecules.

PROSITE

Resource identifying protein families domains and functional sites using diagnostic patterns and profiles.

Pfam

Database of protein families and domains.