Last Update: 08/15/2015
List of Common Bioinformatics Programs:
Detecting Sequence Similarity
Program
Web Address
NCBI BLAST http://blast.ncbi.nlm.nih.gov/Blast.cgi
FlyBase
BLAST
http://flybase.org/blast/
FASTA
http://www.ebi.ac.uk/Tools/sss/fasta/
BLAT
http://genome.ucsc.edu/cgi-bin/hgBlat
Clustal
Omega
http://www.ebi.ac.uk/Tools/msa/clustalo/
Stretcher
https://www.ebi.ac.uk/Tools/psa/emboss_stretcher/
Matcher
http://www.ebi.ac.uk/Tools/psa/emboss_matcher/
Web Databases
Program
Web Address
FlyBase
http://flybase.org
modENCODE http://modencode.org/
UCSC
Genome
Browser
Ensembl
http://genome.ucsc.edu
http://metazoa.ensembl.org/index.html
Purpose
Detect regions of local
similarity between a
query sequence and
sequences in a database
Perform BLAST searches
against multiple
Drosophila species
Suite of programs for
performing global and
local similarity searches
Rapid alignment of query
sequences against a
genome assembly. Less
sensitive than BLAST
Generate global
alignment for multiple
sequences
Use the Needleman and
Wunsch algorithm to
identify the optimal
global alignment between
two sequences
Identify local regions of
similarities between two
input sequences using the
Waterman-Eggert local
alignment algorithm
Purpose
Access the most recent set of
D. melanogaster gene annotations
Access data produced by the
modENCODE project
Access genome assemblies and
annotations generated by UCSC
(e.g., Human, Chimpanzee)
Access genome assemblies and
annotations for different insects.
Users can easily retrieve individual
exon sequences using the Ensembl
interface
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Last Update: 08/15/2015
Gene Predictors
Program
Web Address
Genscan
http://genes.mit.edu/GENSCAN.html
Augustus
http://bioinf.uni-greifswald.de/augustus/
Repeat Finders
Program
Web Address
RepeatMasker http://www.repeatmasker.org
CENSOR
http://www.girinst.org/censor/index.php
Purpose
ab initio gene predictor
(optimized for mammalian
genome)
ab initio and evidence-based
gene predictor
Purpose
Find interspersed repeats and
low complexity DNA in the
query sequence
Identify matches in a query
sequence to known repeats in
RepBase
Motif Finding
Program
Web Address
Fly Factor
http://mccb.umassmed.edu/ffs/
Survey
Patser
MEME
Suite
Purpose
Database of
transcription factor
binding sites in
D. melanogaster
http://stormo.wustl.edu/consensus/html/Html/main.html Search for matches to
conserved motifs
http://meme-suite.org/
Suite of tools for motif
discovery and analysis
Sequence Analysis Tools
Program
Web Address
EMBOSS
http://emboss.bioinformatics.nl/
Tools
Purpose
Large collection of
bioinformatics tools for
manipulating and analyzing
sequences (e.g. translation,
extract subsequence)
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