bioinformatics 2

Bioinformatics vs. genomics

Bioinformatics uses computing and data analysis to interpret biological information; genomics studies complete genomes and genome-scale structure function variation and evolution.

Genetics vs. genomics

Genetics often examines individual genes and inherited traits; genomics examines many genes or entire genomes.

Bioinformatics applications

Sequence alignment; database searching; genome assembly; gene prediction; annotation; gene-expression analysis; metagenomics; and comparative genomics.

Python vs. C

Python is readable and fast to develop with; C is compiled and often faster and more memory-efficient for processing large datasets.

C++ vs. R

C++ provides high performance for developing software tools; R specializes in statistics and visualization.

Perl vs. Bash

Perl is historically important for sequence and text processing; Bash automates Unix commands and pipelines.

Sequence alignment

Places DNA RNA or protein sequences alongside each other to compare identities differences conserved positions insertions and deletions.

Global vs. local alignment

Global aligns the full lengths of both sequences; local finds the best matching region within them.

Needle and Needleman-Wunsch

Needle uses the Needleman-Wunsch algorithm for global alignment; choose it when most of both sequences are related.

Water and Smith-Waterman

Water uses the Smith-Waterman algorithm for local alignment; choose it when only part of the sequences may match such as a conserved domain.

Conserved positions and indels

Conserved positions stay similar across aligned sequences; insertions or deletions may appear as gaps.

Substitution matrix

Scores amino acid matches and replacements based on how often substitutions are observed relative to chance.

PAM matrices

Point Accepted Mutation matrices are based on substitutions in closely related proteins; PAM1 is a small evolutionary distance and higher PAM numbers represent greater divergence.

BLOSUM matrices

BLOcks SUbstitution Matrices are based on conserved protein-family blocks; BLOSUM62 is commonly used and lower BLOSUM numbers are suited to more divergent sequences.

PAM vs. BLOSUM numbering

Higher PAM number means more divergence; lower BLOSUM number means more divergence.

Positive zero and negative matrix scores

Positive means substitution is more common than chance; zero means about as common as chance; negative means less common than chance.

Dot plot

Visual comparison that marks matching sequence positions and reveals similarity and structural patterns.

Dot plot diagonal patterns

Long diagonal means similarity; broken diagonal suggests an insertion or deletion; parallel diagonals suggest repeats; reverse diagonal suggests inversion.

BLAST

Basic Local Alignment Search Tool; a fast heuristic search for local similarities between a query sequence and database sequences.

Query sequence and BLAST hit

Query is the submitted sequence; a hit is a database sequence that produces an alignment with the query.

blastn vs. blastp

blastn compares nucleotide query to nucleotide database; blastp compares protein query to protein database.

blastx

Translates a nucleotide query and searches a protein database.

tblastn

Compares a protein query to a translated nucleotide database.

tblastx

Compares translated nucleotide queries with translated nucleotide database sequences.

BLAST percent identity and query coverage

Percent identity is the percentage of exactly matching aligned positions; query coverage is the fraction of the query included in the alignment.

BLAST bit score and E-value

Higher bit score means a stronger-scoring alignment; lower E-value means fewer matches of that score are expected by chance and therefore greater statistical significance.

BLASTP alignment symbols

Amino acid letter in the middle line means exact match; plus sign means positive-scoring conservative substitution; blank means mismatch; dash means gap.

Unix

Operating system environment used to manage files and run command-line bioinformatics tools.

pwd ls and cd

pwd prints the current directory; ls lists files and folders; cd changes directories.

mkdir cp mv and rm

mkdir creates a directory; cp copies a file; mv moves or renames a file; rm deletes a file.

cat less head and tail

cat displays file contents; less scrolls through text; head shows the first lines; tail shows the last lines.

grep and wc -l

grep searches for matching text or patterns; wc -l counts lines.

curl and tar

curl retrieves data from a URL; tar creates or extracts archives.

FASTA file and header

FASTA is a text format for biological sequences; each sequence begins with a header line starting with > followed by sequence letters.

Count FASTA sequences with grep

grep -c '^>' sequences.fasta counts lines starting with > and therefore counts sequences.

Unix output redirection > and >>

writes output to a file and overwrites existing contents; >> appends output to the end of a file.

Unix pipe |

Sends one command's output into another command; for example grep '^>' sequences.fasta | wc -l counts FASTA headers.

Extract vs. create tar archives

tar -xvf files.tar extracts an archive; tar -cvf files.tar folder/ creates one.

Extract vs. create compressed tar.gz archives

tar -xzvf files.tar.gz extracts a compressed archive; tar -czvf files.tar.gz folder/ creates one.

SeqKit

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

seqkit stats and seqkit grep

seqkit stats reports sequence counts and length statistics; seqkit grep finds or extracts matching records.

seqkit subseq and seqkit sort -l

seqkit subseq extracts sequence regions; seqkit sort -l sorts sequences by length.

seqkit fx2tab -n -g and GC content

Command displays sequence names and GC content; GC content is the proportion of bases that are G or C.

Reverse complement

Reverse the nucleotide sequence order and replace each base with its complement; the study guide asks you to know how to do this using SeqKit.

UniProt

Database of protein sequences and functional annotations including curated names functions and cross-references.

PDB

Protein Data Bank; stores experimentally determined three-dimensional structures of proteins nucleic acids and complexes.

PROSITE

Database of protein families domains and functional sites represented by diagnostic patterns and profiles.

Pfam

Database used to identify protein families and domains.

InterPro

Integrates protein-signature resources including Pfam and PROSITE to annotate protein families domains and functional sites.