SDSC Biology Workbench

http://workbench.sdsc.edu/

GENOME BROWSERS

http://www.ensembl.org/index.html

NASONIA GENOME PROJECT

http://www.hgsc.bcm.tmc.edu/projects/nasonia/

HONEY BEE GENOME RESOURCES

http://www.ncbi.nlm.nih.gov/projects/genome/guide/bee/

HONEYBEE GENOME PROJECT

http://www.hgsc.bcm.tmc.edu/projects/honeybee/

BIOLOGICAL INFORMATION RESOURCE (U of Washington)

http://courses.washington.edu/bioinfo/BIR/

123 GENOMICS

http://www.123genomics.com/files/analysis.html

GENERIC MODEL ORGANISM DATABASE PROJECT

http://www.gmod.org/home

INFORMATICS CORE LAB

http://www.infosci.coh.org/corelab/sequence_analysis.asp?parent=genomics&child=sequence

SOCKEYE

http://www.bcgsc.ca/project/bomge/sockeye/

COLORADO STATE MOLECULAR TOOLKIT

http://www.vivo.colostate.edu/molkit/index.html

ENTREZ

http://www.ncbi.nlm.nih.gov/gquery/gquery.fcgi

Primer 3

http://fokker.wi.mit.edu/cgi-bin/primer3/primer3_www.cgi

Integrated DNA technologies: Sci Tools

http://www.idtdna.com/SciTools/SciTools.aspx

Integrated DNA technologies: Tech Vault

http://www.idtdna.com/TechVault/Technical.aspx

Sequence Massager

http://www.attotron.com/cybertory/analysis/seqMassager.htm

Sequence Extractor

http://bioinformatics.org/seqext/

Sequence Manipulation Suite

http://bioinformatics.org/sms2/about.html

Drosophila: Gene Analysis Tools

http://www.fruitfly.org/seq_tools/other.html

RNA and splice sites

http://www.clfs.umd.edu/labs/mount/RNAinfo/

http://www.fruitfly.org/seq_tools/splice.html

http://bcc20.caspur.it/ccb/en/Tools/ASPIC

High Throughput Computing for Alternative Splicing Prediction

http://t.caspur.it/HTC4aspic/

Finding Open Reading Frames

http://bioinformatics.org/sms2/orf_find.html

http://bioinformatics.org/sms/orf_find.html

http://www.vivo.colostate.edu/molkit/translate/index.html

Protein Motiff

SMART

http://smart.embl-heidelberg.de/Pfam

http://pfam.sanger.ac.uk/

Merge DNA sequences

http://bioweb.pasteur.fr/seqanal/interfaces/merger.html

Clustal W Nucleotide and Amino Acid alignments:

http://www.ebi.ac.uk/Tools/clustalw2/index.html

http://www.genebee.msu.su/services/malign_reduced.html

http://mobyle.pasteur.fr/cgi-bin/MobylePortal/portal.py

Blast 2: Pairwise Blast Alignment

http://www.ncbi.nlm.nih.gov/blast/bl2seq/wblast2.cgi

Note: play around with the mismatch penalty to see how it affects alignments

Blast search:

http://www.ncbi.nlm.nih.gov/BLAST/

http://www.ncbi.nlm.nih.gov/Education/BLASTinfo/information3.html

Sequence Utilities Including Translation and Reverse Complement

http://searchlauncher.bcm.tmc.edu/seq-util/seq-util.html

Translating your sequence:

http://www.expasy.ch/tools/dna.html

http://www.ebi.ac.uk/Tools/emboss/transeq/

Standard Genetic Code

http://www.ebi.ac.uk/cgi-bin/mutations/trtables.cgi

Find restriction sites

http://tools.neb.com/NEBcutter2/index.php

Basic Guide to Sequence Analysis -- good intro

http://www.sequenceanalysis.com/contents.html

Nevada Genomics

http://www.ag.unr.edu/genomics/