CODEHOP:
COnsensus-DEgenerate Hybrid Oligonucleotide Primers

PCR primers designed from protein multiple sequence alignments

• Getting started
• Full Help file
• The CODEHOP algorithm
• The CODEHOP manuscript
• Genes identified using CODEHOP

• The input should be a set of local multiple alignments (blocks) of a group of related protein sequences. The alignments must be in Blocks Database format, such as in Block Maker
output.
• Ungapped parts of Clustal- or FASTA-formatted global multiple alignments can be automatically turned into blocks by the Blocks multiple alignment processor. You can also manually reformat multiple sequence alignments with the Blocks formatter.
• The output of all these programs contains links that send the resulting blocks to this page.
• If your sequences align globally, you will get better multiple alignment results from Clustal than from the motif finders used by Block Maker.
• Blocks are processed using sequence weights (the numbers following each sequence segment). To emphasize particular sequences in the block(s) manually adjust the sequence weights. Increase the number to give a sequence more weight.

Genetic code Standard Vertebrate Mitochondrial Yeast Mitochondrial Mold Mitochondrial and Mycoplasma Invertebrate Mitochondrial Ciliate Nuclear Echinoderm Mitochondrial Euplotid Mitochondrial Bacterial and Plant Plastid Alternative Yeast Nuclear Ascidian Mitochondrial Flatworm Mitochondrial Blepharisma Macronuclear Chlorophycean Mitochondrial Trematode Mitochondrial Scenedesmus obliquus Mitochondrial Thraustochytrium Mitochondrial

Codon usage table (scroll for more choices): ------gbbct------ Acholeplasma laidlawii Agrobacterium tumefaciens Bacillus subtilis Bacillus thuringiensis Bartonella bacilliformis Bartonella henselae Brucella abortus Burkholderia glumae Campylobacter jejuni Chlamydia trachomatis Chlorobium limicola Chlorobium vibrioforme Chlorobium tepidum Clostridium botulinum Colwellia psychrerythraea 34H Crenarchaeota Ehrlichia chaffeensis Escherichia coli Euryarchaeota Haemophilus influenzae Halobacterium sp. NRC-1 Helicobacter pylori 26695 Lactobacillus casei Lactococcus lactis subsp. lactis Il1403 Leptospira interrogans Micrococcus luteus Myxococcus xanthus Notophthalmus viridescens Pantoea agglomerans Paracoccus denitrificans Picrophilus torridus Pseudoalteromonas atlantica T6c Pseudomonas syringae pv. glycinea Pyrococcus horikoshii OT3 Ralstonia eutropha Rhizobium leguminosarum Rhodobacter sphaeroides Rhodococcus erythropolis Serratia marcescens Shewanella oneidensis MR-1 Sinorhizobium meliloti Staphylococcus aureus Streptomyces coelicolor Sulfolobus solfataricus Synechococcus sp. Unknown flavobacteria Variovorax paradoxus Vibrio cholerae O1 biovar eltor str. N16961 Vibrio fischeri ES114 Xanthomonas oryzae pv. oryzae ------gbinv------ Acanthamoeba castellanii Acropora millepora Ancylostoma canium Anopheles gambiae Anopheles stephensi Apis mellifera Aplysia californica Artemia franciscana Ascaris suum Bivalve mollusks Blattella germanica Bombyx mori Brugia malayi Caenorhabditis elegans Callinectes sapidus Cephalopods Cotesia congregata Cryptosporidium parvum Culex pipiens Culicoides sonorensis Dictyostelium discoideum Drosophila melanogaster Encephalitozoon cuniculi GB-M1 Entamoeba histolytica Galleria mellonella Geodia cydonium Giardia intestinalis Haemonchus contortus Helicoverpa armigera Heliothis virescens Heterodera glycines Hirudo medicinalis Hydra vulgaris Lasius niger Leishmania major Leishmania tarentolae Litopenaeus vannamei Lucilia cuprina Lymnaea stagnalis Musca domestica Mytilus edulis Mytilus galloprovincialis Myzus persicae Onchocerca volvulus Placopecten magellanicus Plasmodium falciparum Podocoryne carnea Rhipicephalus microplus Schistosoma mansoni Strongylocentrotus purpuratus Suberites domuncula Tetrahymena pyriformis Tetrahymena thermophila Trichinella spiralis Trichomonas vaginalis Trypanosoma brucei ------gbmam------ Bos taurus Canis familiaris Equus caballus Oryctolagus cuniculus Ovis aries Sus scrofa ------gbpln------ Alnus glutinosa Antirrhinum majus Arabadopsis thaliana Aspergillus fumigatus Aspergillus nidulans Bixa orellana Brassica napus Brassica oleracea Camptotheca acuminata Ceratopteris richardii Chara corallina Chlamydomonas reinhardtii Citrus sinensis Clarkia breweri Clarkia concinna Corylus avellana Cucumis sativus Dunaliella salina Emericella nidulans Eschscholzia californica Euglena gracilis Fabaceae family Gerbera hybrid cultivar Gerbera hybrid cv. 'Terra Regina' Ginkgo biloba Glycine max Gonyaulax polyedra Gossypium hirsutum Hordeum vulgare Hortaea werneckii Lotus corniculatus var. japonicus Lilium longiflorum Lycopersicon esculentum Malus domestica Manihot esculenta Marchantia polymorpha Medicago truncatula Mesembryanthemum crystallinum Mucor circinelloides Mucor racemosus Musa acuminata Neurospora crassa Nicotiana tabacum Oryza sativa Petunia x hybrida Phaseolus vulgaris Physcomitrella patens Pichia angusta Pichia pastoris Pinus strobus Pinus sylvestris Pinus taeda Pisum sativum Pleurotus ostreatus Porphyra pulchra Porphyra yezoensis Prunus persica Ricinus communis Saccharomyces cerevisiae Schizosaccharomyces pombe Sclerotinia sclerotiorum Silene latifolia Solanum tuberosum Sorghum bicolor Trametes versicolor Triticum aestivum Uncinula necator Ustilago maydis Vitis vinifera Zea mays Zingiber officinale Zinnia elegans ------gbpri------ Homo sapiens ------gbrod------ Cavia porcellus Mus musculus Rattus norvegicus ------gbvrl------ Banana bunchy top virus Chilo iridescent virus Grapevine leafroll-associated virus 2 Human herpesvirus 4 Papaya ringspot virus Vesicular stomatitis virus ------gbvrt------ Ambystoma mexicanum Anas platyrhynchos Cairina moschata Crotalus atrox Danio rerio Eptatretus stouti Fugu rubripes Gallus gallus Ginglymostoma cirratum Ictalurus punctatus Myxine glutinosa Petromyzon marinus Platichthys flesus Trachemys scripta Squalus acanthias Xenopus laevis ------other------ Equal

By default, up to 3 of the least degenerate primers in an overlapping set are shown.

Show the least degenerate, or show all overlapping primers.

By default, the 3' base of the primer must be an invariant position, regardless of the core strictness setting.
Use core strictness for the 3' base.

Force the core/clamp boundary to be a codon boundary. Use the most common codons in the clamp.