Gene finders
Similarity finders
DNA feature finders
Protein feature finders
Pattern finders
Miscellaneous tools
Commercial sites

Gene Finders

• TestCode [GCG]

Provides general predictions of which regions within a DNA sequence encodes protein. Cannot identify precise termini of protein-encoding regions. Based mostly on codon bias, but does not require the user to provide codon frequency table.
Ref: Fickett J (1982) Nucl Acids Res 10:5303-5318.
 
• FGeneSH (w/donor GC) [http://www.softberry.com/berry.phtml?topic=gfind]

Good for eukaryotic genomic sequences. Uses hidden Markov model (HMM), trained on humans, Drosophila, C. elegans, and plants (you specify) to predict exons and introns. Assembles best guess at translated sequence. Easy to use.
Ref: Salamov A.A., Solovyev V.V. (1999), unpublished data. "Please, reference: Computational Genomics Group (Sanger Centre) WEB server."Maybe Salamov AA Solovyev VV (2000) Genome Res 10:516-22.
 
• BestOrf[http://genomic.sanger.ac.uk/gf/gf.html]

Good for eukaryotic cDNA sequences. Uses Markov analysis, trained on humans and plants (you specify) to predict translated sequence. Accuracy nearly 100%, thus depends on the quality of the EST or cDNA sequence you provide.
Ref: Solovyev V.V., Salamov A.A., unpublished data.
 
• Grail[http://compbio.ornl.gov/Grail-1.3/]

Good for eukaryotic genomic sequences. I've never used it and it is included here only for completeness because it is a very popular program.
 
• GeneMark [http://opal.biology.gatech.edu/GeneMark/]

Good for prokaryotic sequences or eukaryotic sequences Uses Markov models based on (your choice) training on specific genomes (many!) or on general features of translational start sites.
Ref: Lukashin A, Borodovsky M (1998) Nucl Acids Res 26:1107-1115; Besemer J, Lomsadze A, Borodovsky M (2001) Nucl Acids Res 29:2607-2618.
 
• FRAMES [GCG]

Simple minded program that can be used on any sequence. Finds every open reading frame beginning with a start codon and ending with a stop codon. For eukaryotic sequences, specify the -ALL command line parameter to force display of all stop codons (otherwise only the first after a start codon is shown). Still, the program is of limited utility with eukaryotic sequences.
 
• MAP [GCG]

Displays translation of any sequence in one or more of the six possible reading frames. Will show stop codons as "*" but go right on translating. The program is really designed to list restriction sites, but if you just want the translation, give NotI (for AT-rich sequences) or SwaI (for GC-rich sequences) as the enzyme to be mapped. There will probably be no sites and thus no clutter.

• Orf Finder [http://www.ncbi.nlm.nih.gov/gorf/]

Like Frames (above) but much nicer user interface. Finds every open reading frame within a (max) 30 kb segment of DNA, without regard to its source. Scans through all six possible reading frames looking for long stretches between start codons and stop codons. Clicking on an ORF gets you to the predicted amino acid sequence and to BLAST. May have problem if gene does not begin with ATG.

• BLAST (Basic local alignment search tool) [http://www.ncbi.nlm.nih.gov/BLAST/]

Compares DNA or protein sequences against nonreduntant or other databases. It comes in different flavors (see below). Graphical output allows you to see at a glance the region of the query that is similar for each hit -- very valuable information.
Ref: Altschul SF, Madden TL Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Nucl Acids Res 25:3389-3402.

• BlastP: Compares your protein sequence against a database of protein sequences. You'll probably use this most often, or derivatives of it (Psi-BLAST or Phi-BLAST). Also provides results from a CD (conserved domain)-Search of Pfam motifs, which is often worth the price of admission by itself.
• BlastN: Compares your DNA sequence against a database of DNA sequences. Use this if you're interested in finding conserved DNA features, such as transposon ends or regulatory sites. If you want to find what gene may be contained within your DNA sequence, use BlastX.
• BlastX: Translates your DNA sequence in all six possible reading frames and compares the resulting amino acid sequences against a database of protein sequences.
• Blast 2 sequences: Compares your DNA or protein sequence against another of your DNA or protein sequences. This is a quick way of getting an alignment of two sequences.

• FastA [http://www.genome.ad.jp/]

(May the gods and/or Bill Pearson strike me dead, but I confess I haven't used it)

• Within BLAST (any flavor), scroll down to "Options for advanced blasting". On the line beginning "Limit by…" select the desired class of organisms from the pull down menu at the right. Or (same line) specify a key word (like the name of the species) in the box to the left. This latter choice provides a very leaky filter.

 
• To search only ESTs (expresses sequence tags; cDNAs) within BLASTN, click arrow by the box next to "Choose database" and select "est_human" (or whatever database is appropriate).

 
• Find an organism-specific web site. There are many lists of such sites. Here are some (please pardon my ignorance of eukaryotes):

• Prokaryotic Ongoing Genome Projects [http://ergo.integratedgenomics.com/GOLD/prokaryagenomes.html]

A couple of hundred sites (only some with search capabilities) but URLs often out of date (who can blame them?)
• TIGR (The Institute of Genomic Research) Comprehensive Microbial Database

[http://www.tigr.org/tigr-scripts/CMR2/CMRHomePage.spl]
Several dozen sites, all accessible through a standard interface.
• Go on line (e.g. www.google.com) and search for [your favorite organism] + "genome"

Just about every sequenced genome has its own site nowadays.

• TSSW (Transcriptional Start Site - Wingender) [http://www.softberry.com/berry.phtml?topic=promoter]

Predicts eukaryotic transcriptional start sites (called in output "promoters") for RNA Polymerase II using Wingender's database of conserved elements. Claims that it will recognize about 50% of true promoters and give a false positive once every 4000 bp.
Ref: Solovyev V.V., Salamov A.A., Lawrence C.B. (unpublished).
 
• BProm[http://www.softberry.com/berry.phtml?topic=promoter]

Predicts prokaryotic promoter sites. Claims that it will recognize about 80% of true E. coli sigma-70 promoters. Advises that program be used only on intergenic regions.Warning: no reference given, and algorithm not explained!
 
• PolyAH[http://www.softberry.com/berry.phtml?topic=promoter]

Predicts eukaryotic polyA processing sites, with program trained on collection of human sequences containing bona fide AATAAA processing signal. Claims (with appropriate threshold value) finds 86% correct sites with 8% false positives.
Ref: Salamov AA, Solovyev VV (1997). Computer Applic Biosci 13:23-28.
 
• Tandem Repeats Finder [http://tandem.bu.edu/trf/trf.submit.options.html]

Finds tandem DNA repeats (repeated sequences that occur one after another). Can work on huge chunks of DNA at one time and find repeated sequences with a periodicity between 1 and 500 nucleotides (no need for user to specify size). Permits short gaps between repeats.
Ref: Benson G (1999) Nucl Acids Res 27:573-580.
 
• REPEATS [GCG]

Finds repeats in DNA or protein sequences, where the sequences occur within a distance specified by the user (so may be tandem or separated by hundreds of bases). Works by simple comparisons, like a dot plot. You need to specify the window size (the minimum length of the repeats to be found) and the stringency (the number of allowed mismatches).
 
• TERMINATOR [GCG]

Predicts positions of prokaryotic transcriptional terminators by comparison with set of known terminators.
Ref: Brendel V, Trifonov EN (1984) Nucl Acids Res 12:4411-4427.
 
• TIGR Software Tools[http://www.tigr.org/softlab/]

Treasure trove of free, downloadable software to find transcriptional terminators, splice sites, coding regions, ribosome binding sites, and vector sequences (to be removed from new sequences).
 
• WebLogo [http://www.bio.cam.ac.uk/cgi-bin/seqlogo/logo.cgi]

Represents information content of aligned sequences as height. Tells you much more than mere consensus sequences.

• DAS (Dense alignment surface method) [http://www.sbc.su.se/~miklos/DAS/]

Predicts transmembrane regions. Performs dot plots against collection of archtypical transmembrane protein.
Ref: Cserzo M, Wallin E, Simon I, von Heijne G, and Elofsson A (1997). Prot Engineering 10:673-676
 
• Pfam (protein families) [http://pfam.wustl.edu/]

Predicts motifs within amino acid sequences by comparison against a database of consensus sequences.
Ref: Bateman A, Birney E, Durbin E, Eddy SR, Howe KL, Sonnhammer ELL (2000) Nucl Acids Res 28:263-266.
 
• SMART (Simple modular architecture research tool) [http://smart.embl-heidelberg.de/]

Predicts motifs within amino acid sequences by comparison against a database of consensus sequences. Sounds like Pfam? SMART uses a different database, biased towards regulatory motifs, that only partially overlaps with that used by Pfam. Actually, SMART is a suite of separate programs, allowing you to get different kinds of structural information.
Ref: Letunic I et al (2002) Nucl Acids Res 30:242-244.
 
• BLASTP(and derivatives) [http://www.ncbi.nlm.nih.gov/BLAST/]

BLAST searches automatically give you searches through Pfam and SMART databases (they call it CD-Searches (CD = Conserved Domain). Very convenient, but for some reason you don't always get the same answers as separate searches through Pfam and SMART.
Ref: Marchler-Bauer A., Panchenko AR, Shoemaker BA, Thiessen PA, Geer LY, Bryant SH (2002) Nucl Acids Res 30:281-283.
 
• SignalP v2.0 [http://www.cbs.dtu.dk/services/SignalP-2.0/]

Predicts signal peptide cleavage sites and to a lesser extent membrane anchor peptides. Consists of two programs: SignalP-NN (neural net), better for predicting cleavage sites; and SignalP-hmm (hidden Markov models), better for descriminating between cleavage sites and uncleaved anchor sequences. Trained on (your choice) eukaryotes, Gram negative bacteria, or Gram-positive bacteria.
Ref (Review): Nielsen H, Brunak S, von Heijne G (1999) Protein Engineering 12:3-9.
 
• PILEUP [GCG]

Multiple sequence alignment. Uses a method derived from Clustal (see below). I haven't determined how their results differ except cosmetically.
 
• ClustalW[http://searchlauncher.bcm.tmc.edu/multi-align/multi-align.html]

Multiple sequence alignment. First constructs phylogenetic tree by pairwise comparisons, then aligns sequences with aid of tree. Sometimes fails with sequences whose similarity is masked by large regions of dissimilarity. For Windows users who want to download their own free copy of Clustal (ClustalX) and get much prettier output than obtained from either PILEUP or ClustalW, look at the second reference below.
Ref: (ClustalW) Thompson JD, Higgins DG, Gibson TJ (1994) Nucl Acids Res 22:4673-4680
(ClustalX) Thompson JD et al (1997) Nucl Acids Res 25:4876-4882.
 
• ExPASy Proteomics Tools [http://www.expasy.ch/tools/]

A variety of useful tools to characterize peptide sequences (e.g. mass, protease cleavage products, etc) and to identify proteins from those characteristics. It also provides tools for secondary and tertiary structure analysis and those that predict protein modifications.

• FindPatterns [GCG]

Looks for short, user-specified patterns in DNA sequences. You can use it to find restriction sites, consensus binding sites, etc. It allows ambiguities (by using standard one-letter symbols) and mismatches (by using the -MIS = # of mismatches parameter).

• Consensus [GCG]

Finds nucleotide or amino acid frequencies at each position of a set of sequences that are already aligned. Then, at each position, it lists the most common residue or set of residues whose frequencies sum to a value exceeding a value you specify. You can call this list the consensus sequence.
 
• FitConsensus [GCG]

Uses frequency table made by Consensus (above) to search a sequence for subsequences that best match the frequencies within the table.
Ref: Staden (1984) Nucl Acids Res 12:505-519

• MEME [GCG] and [http://meme.sdsc.edu/meme/website/]

Finds statistically overrepresented motifs in user provided collection of sequences (DNA or protein). If you think you have several genes that probably share an upstream regulatory sequence, the program may find it for you. Or it might find a short amino acid common to a set of protein of similar function (but if the protein are TOO similar, use PILEUP or Clustal). Once you've found one motif or a set of motifs, you can use the MEME-generated prf file (containing the description of the motifs) to search a sequence or set of sequences (e.g. all of PIR) for other instances. In the web version, the program called MAST does the same thing.
 
• Gibbs Motif Sampler [http://bayesweb.wadsworth.org/gibbs/gibbs.html]

Similar in purpose to MEME and works in a very similar way as well. It differs in that it (but not MEME) requires that the user specify the width of the motif sought (i.e., number of amino acids or nucleotides). Also, I think it uses a different strategy to find candidate motifs amongst the huge number possible, so it may find the optimal motif in considerably less time. It overlaps with Meme in its answers, but the answers are not identical.
Ref: Lawrence CE et al (1993) Science 262:208-214.
 
• BioProspector[http://bioprospector.stanford.edu/]

Also similar in purpose to MEME (but works only on DNA sequences, not protein) and also uses Gibbs sampling. However the quality motifs are assessed through zero- to third-order Markov models. The local version (but not the version on the web) supplies estimates of the significance of the motifs found.
Liu X, Brutlag DL, Liu JS (2001). Pac Symp Biocomput. pp127-38.

Miscellaneous Tools

Molecular Toolkit [http://arbl.cvmbs.colostate.edu/molkit/index.html] (Colorado State University)
Many tools for quick manipulation of DNA and protein sequences: Inverse, translate, reverse translate, hydrophobicity plots, dot plots.

Many companies sprung out with the genomic fever, offering integrated gene finding services. Below is a list of some of these companies (in alphabetical order). They are still evolving, some might continue this line of business the market permitting, others might turn into pharmaceutical companies on their own and others might simply disappear. The list is just for your information and in no way implies an endorsement from our part on any of them.

Celera Discovery System (CDS) [http://www.celera.com/index.cfmhttp://www.celera.com/index.cfm], Celera Genomics.

LifeSeq^®[http://www.incyte.com/#], Incyte Genomics.

genomeSCOUT^®[http://www.lionbioscience.com/solutions/genomescout], LION Bioscience.

Rosetta Resolver^® System [http://www.rosettabio.com/home.html], Rosetta Inpharmatics (acquired by Merck).