HMMER Tutorial

Organisms

All organisms

Aethina tumida

Agrilus planipennis

Amyelois transitella

Anabrus simplex

Anastrepha ludens

Anastrepha obliqua

Anoplophora glabripennis

Anthonomus grandis

Apis mellifera

Athalia rosae

Bactrocera dorsalis

Bactrocera oleae

Bemisia tabaci

Blattella germanica

Bombus affinis

Bombus huntii

Bombus impatiens

Bombus terrestris

Bradysia coprophila

Catajapyx aquilonaris

Centruroides sculpturatus

Cephus cinctus

Ceratitis capitata

Chelonus insularis

Cimex lectularius

Clitarchus hookeri

Contarinia nasturtii

Copidosoma floridanum

Cydia pomonella

Cylas formicarius

Dermacentor andersoni

Diabrotica virgifera

Diachasma alloeum

Diachasmimorpha longicaudata

Diaphorina citri

Diorhabda carinulata

Diorhabda sublineata

Diprion similis

Drosophila biarmipes

Drosophila bipectinata

Drosophila elegans

Drosophila eugracilis

Drosophila ficusphila

Drosophila kikkawai

Drosophila rhopaloa

Drosophila takahashii

Dufourea novaeangliae

Ephemera danica

Eufriesea mexicana

Euglossa dilemma

Eurytemora affinis

Fopius arisanus

Frankliniella occidentalis

Galleria mellonella

Gerris buenoi

Habropoda laboriosa

Halyomorpha halys

Helicoverpa zea

Heliothis virescens

Holacanthella duospinosa

Homalodisca vitripennis

Hyalella azteca

Hylaeus anthracinus

Hylaeus volcanicus

Ladona fulva

Laodelphax striatellus

Lasioglossum albipes

Latrodectus hesperus

Leguminivora glycinivorella

Leptinotarsa decemlineata

Limnephilus lunatus

Locusta migratoria

Loxosceles reclusa

Lucilia sericata

Mamestra configurata

Manduca sexta

Mayetiola destructor

Medauroidea extradentata

Megachile rotundata

Melipona quadrifasciata

Microplitis demolitor

Microplitis mediator

Neodiprion fabricii

Neodiprion lecontei

Neodiprion pinetum

Neodiprion virginiana

Nicrophorus vespilloides

Nylanderia fulva

Odontomachus brunneus

Oncopeltus fasciatus

Onthophagus taurus

Ornithodoros turicata

Orussus abietinus

Osmia lignaria

Pachypsylla venusta

Parasteatoda tepidariorum

Pectinophora gossypiella

Peregrinus maidis

Photinus pyralis

Plodia interpunctella

Rhagoletis zephyria

Rhipicephalus microplus

Schistocerca americana

Schistocerca cancellata

Schistocerca gregaria

Schistocerca nitens

Schistocerca piceifrons

Schistocerca serialis

Tigriopus californicus

Tribolium castaneum

Tribolium madens

Trichogramma pretiosum

Vanessa tameamea

Varroa destructor

Varroa jacobsoni

Venturia canescens

Vespa mandarinia

Zeugodacus cucurbitae

All organisms

Peptide

Protein - 151 databases

Aethina tumida

Protein

Protein - Aethina tumida NCBI Annotation release 101, translated CDS

Agrilus planipennis

Protein

Protein - Agrilus planipennis NCBI Annotation release 101, translated CDS

Amyelois transitella

Protein

Protein - Amyelois transitella NCBI Annotation release GCF_032362555.1-RS_2023_11, translated CDS

Anabrus simplex

Protein

Protein - Anabrus simplex NCBI Annotation release GCF_040414725.1-RS_2024_09, translated CDS

Anastrepha ludens

Protein

Protein - Anastrepha ludens NCBI Annotation release GCF_028408465.1-RS_2023_03, translated CDS

Anastrepha obliqua

Protein

Protein - Anastrepha obliqua NCBI Annotation release GCF_027943255.1-RS_2023_03, translated CDS

Anoplophora glabripennis

Protein

Protein - NCBI Anoplophora glabripennis Annotation Release 101, translated CDS

Protein - Anoplophora glabripennis peptides, OGSv1.2

Protein - Anoplophora glabripennis OGSv1.3, peptides

Anthonomus grandis

Protein

Protein - Anthonomus grandis grandis NCBI Annotation release 100, translated CDS

Apis mellifera

Protein

Protein - Apis mellifera NCBI Annotation release 104, translated CDS

Protein - Apis mellifera OGSv3.4, translated CDS

Athalia rosae

Protein

Protein - Athalia rosae NCBI Annotation release 103, translated CDS

Protein - Athalia rosae OGS_v1.3, translated CDS

Bactrocera dorsalis

Protein

Protein - Bactrocera dorsalis Bdor_v1 MAKER annotations - BDOR1.1, translated CDS

Protein - Bactrocera dorsalis NCBI Annotation release 103, translated CDS

Bactrocera oleae

Protein

Protein - Bactrocera oleae NCBI Annotation release 101, translated CDS

Protein - Bactrocera oleae JAMg_OGSv1.1, translated CDS

Bemisia tabaci

Protein

Protein - Bemisia tabaci Annotation Release 100 (GCF_001854935.1), proteins

Protein - Bemisia tabaci OGS MEAM1_v1.2, proteins

Blattella germanica

Protein

Protein - Blattella_germanica_BCM_v0.5.3_proteins

Protein - Blattella germanica OGSv1.2, peptides

Bombus affinis

Protein

Protein - Bombus affinis NCBI Annotation release 100, translated CDS

Bombus huntii

Protein

Protein - Bombus huntii NCBI Annotation release 100, translated CDS

Bombus impatiens

Protein

Protein - Bombus impatiens NCBI Annotation release 103, translated CDS

Protein - Bombus impatiens OGSv1.1, peptide

Bombus terrestris

Protein

Protein - Bombus terrestris NCBI Annotation release 103, translated CDS

Bradysia coprophila

Protein

Protein - Bradysia_coprophila.Bcop_v1.0, proteins

Protein - Bradysia coprophila NCBI Annotation release 100, translated CDS

Catajapyx aquilonaris

Protein

Protein - Catajapyx aquilonaris BCM 0.5.3, translated CDS

Centruroides sculpturatus

Protein

Protein - Centruroides sculpturatus NCBI Annotation release 100, translated CDS

Cephus cinctus

Protein

Protein - Cephus cinctus NCBI Annotation release 101, translated CDS

Protein - Cephus cinctus cepcin_OGSv1.2, translated CDS

Ceratitis capitata

Protein

Protein - Ceratitis capitata NCBI Annotation release 103, translated CDS

Protein - Ceratitis capitata OGS release 1.1, translated CDS

Chelonus insularis

Protein

Protein - Chelonus insularis NCBI Annotation Release 100, translated CDS

Cimex lectularius

Protein

Protein - Cimex lectularius NCBI annotation release 101, peptide

Protein - Cimex lectularius OGS v1.2, peptides

Clitarchus hookeri

Protein

Protein - Clitarchus hookeri Maker annotations, proteins

Contarinia nasturtii

Protein

Protein - Contarinia nasturtii NCBI Annotation Release 100, translated CDS

Copidosoma floridanum

Protein

Protein - Copidosoma floridanum NCBI Annotation release 101, translated CDS

Cydia pomonella

Protein

Protein - Cydia pomonella NCBI Annotation release GCF_033807575.1-RS_2023_12, translated CDS

Cylas formicarius

Protein

Protein - Cylas formicarius NCBI Annotation release GCF_029955315.1-RS_2023_10, translated CDS

Dermacentor andersoni

Protein

Protein - Dermacentor andersoni NCBI Annotation release 100, translated CDS

Diabrotica virgifera

Protein

Protein - Diabrotica virgifera Annotation Release 100 (GCF_003013835.1), translated CDS predicted from genomic sequence

Diachasma alloeum

Protein

Protein - Diachasma alloeum Annotation Release 100 (GCF_001412515.1), proteins

Protein - Diachasma alloeum NCBI Annotation Release 101, translated CDS

Diachasmimorpha longicaudata

Protein

Protein - Diachasmimorpha longicaudata NCBI Annotation release GCF_034640455.1-RS_2024_03, translated CDS

Diaphorina citri

Protein

Protein - Diaphorina citri OGSv1.0, proteins

Protein - Diacit_RefSeq_proteins_Release_100

Protein - Diacit_International_psyllid_consortium_proteins_v1

Diorhabda carinulata

Protein

Protein - Diorhabda carinulata NCBI Annotation release GCF_026250575.1-RS_2023_06, translated CDS

Diorhabda sublineata

Protein

Protein - Diorhabda sublineata NCBI Annotation release GCF_026230105.1-RS_2023_05, translated CDS

Diprion similis

Protein

Protein - Diprion similis NCBI Annotation release 100, translated CDS

Drosophila biarmipes

Protein

Protein - Drosophila biarmipes NCBI Annotation release 103, translated CDS

Drosophila bipectinata

Protein

Protein - Drosophila bipectinata NCBI Annotation release 102, translated CDS

Drosophila elegans

Protein

Protein - Drosophila elegans NCBI Annotation release 102, translated CDS

Drosophila eugracilis

Protein

Protein - Drosophila eugracilis NCBI Annotation release 102, translated CDS

Drosophila ficusphila

Protein

Protein - Drosophila ficusphila NCBI Annotation release 102, translated CDS

Drosophila kikkawai

Protein

Protein - Drosophila kikkawai NCBI Annotation release 102, translated CDS

Drosophila rhopaloa

Protein

Protein - Drosophila rhopaloa NCBI Annotation release 102, translated CDS

Drosophila takahashii

Protein

Protein - Drosophila takahashii NCBI Annotation release 102, translated CDS

Protein - Drosophila takahashii Maker proteins v0.5.3 (BCM)

Protein - Drosophila takahashii Annotation Release 101 (GCF_000224235.1), proteins

Dufourea novaeangliae

Protein

Protein - Dufourea novaeangliae v1.1, peptide sequences

Protein - NCBI Dufourea novaeangliae Annotation Release 100, proteins

Ephemera danica

Protein

Protein - Ephemera danica ephdan_OGSv1.0, proteins

Eufriesea mexicana

Protein

Protein - Eufriesea mexicana NCBI Annotation release 100, translated CDS

Protein - Eufriesea mexicana OGSv1.3, translated CDS

Euglossa dilemma

Protein

Protein - Euglossa dilemma v1.0, proteins

Eurytemora affinis

Protein

Protein - Eurytemora affinis Maker proteins v0.5.3 (BCM)

Fopius arisanus

Protein

Protein - Fopius arisanus - NCBI annotation release 100, proteins

Frankliniella occidentalis

Protein

Protein - Frankliniella occidentalis NCBI Annotation release 101, translated CDS

Protein - Frankliniella occidentalis OGSv1.2, translated CDS

Galleria mellonella

Protein

Protein - Galleria mellonella NCBI Annotation release GCF_026898425.1-RS_2022_12, translated CDS

Gerris buenoi

Protein

Protein - Gerris buenoi Maker proteins v0.5.3 (BCM)

Protein - Gerris buenoi OGSv1.1, proteins

Habropoda laboriosa

Protein

Protein - Habropoda laboriosa - ASM126327v1 GenBank Annotations, proteins

Halyomorpha halys

Protein

Protein - Halyomorpha halys Official Gene Set v1.2, proteins

Helicoverpa zea

Protein

Protein - Helicoverpa zea NCBI Annotation Release 100, translated CDS

Heliothis virescens

Protein

Protein - Heliothis virescens OGS 1.1, translated CDS

Holacanthella duospinosa

Protein

Protein - Holacanthella duospinosa annotations Holacanthella_duospinosa_annotation v1.0, proteins

Homalodisca vitripennis

Protein

Protein - Homalodisca vitripennis Maker proteins v0.5.3 (BCM)

Hyalella azteca

Protein

Protein - Hyalella azteca NCBI Annotation release 101, translated CDS

Protein - Hyalella azteca OGSv1.3, translated CDS

Hylaeus anthracinus

Protein

Protein - Hylaeus anthracinus NCBI Annotation release GCF_026225885.1-RS_2023_03, translated CDS

Hylaeus volcanicus

Protein

Protein - Hylaeus volcanicus NCBI Annotation release GCF_026283585.1-RS_2023_03, translated CDS

Ladona fulva

Protein

Protein - Ladona fulva Official Gene Set ladful OGSv1.0, translated CDS

Laodelphax striatellus

Protein

Protein - Laodelphax striatellus laostr_OGSv1.2, proteins

Lasioglossum albipes

Protein

Protein - Lasioglossum albipes proteins, Lalb_OGS_v5.42

Latrodectus hesperus

Protein

Protein - Latrodectus hesperus Maker proteins v0.5.3 (BCM)

Leguminivora glycinivorella

Protein

Protein - Leguminivora glycinivorella NCBI Annotation release 100, translated CDS

Leptinotarsa decemlineata

Protein

Protein - Leptinotarsa decemlineata Maker proteins v0.5.3 (BCM)

Protein - Leptinotarsa decemlineata OGSv1.2, proteins

Limnephilus lunatus

Protein

Protein - Limnephilus lunatus Maker proteins v0.5.3 (BCM)

Locusta migratoria

Protein

Protein - Locusta migratoria JAMg OGS v1, proteins

Loxosceles reclusa

Protein

Protein - Loxosceles reclusa Maker proteins v0.5.3 (BCM)

Lucilia sericata

Protein

Protein - Lucilia sericata NCBI Annotation release 100, translated CDS

Mamestra configurata

Protein

Protein - Mamestra configurata (GCA_002192655.3), translated CDS

Manduca sexta

Protein

Protein - Manduca sexta NCBI Annotation release 102, translated CDS

Protein - Manduca_sexta_OGS_v2.0_peptide

Mayetiola destructor

Protein

Protein - Mayetiola destructor OGS_v1.0, proteins

Medauroidea extradentata

Protein

Protein - Medauroidea extradentata annotations OGS v1.0, proteins

Megachile rotundata

Protein

Protein - Megachile rotundata v1.1, proteins

Protein - Megachile rotundata NCBI annotation release 101, proteins

Melipona quadrifasciata

Protein

Protein - Melipona quadrifasciata GLEAN predicted proteins

Protein - Melipona quadrifasciata v1.1. proteins

Microplitis demolitor

Protein

Protein - Microplitis demolitor NCBI Annotation release GCF_026212275.2-RS_2023_02, translated CDS

Microplitis mediator

Protein

Protein - Microplitis mediator NCBI Annotation release GCF_029852145.1-RS_2023_06, translated CDS

Neodiprion fabricii

Protein

Protein - Neodiprion fabricii NCBI Annotation release 100, translated CDS

Neodiprion lecontei

Protein

Protein - Neodiprion lecontei NCBI Annotation release 101, translated CDS

Neodiprion pinetum

Protein

Protein - Neodiprion pinetum NCBI Annotation release 100, translated CDS

Neodiprion virginiana

Protein

Protein - Neodiprion virginiana NCBI Annotation release 100, translated CDS

Nicrophorus vespilloides

Protein

Protein - Nicrophorus vespilloides Annotation Release 100 (GCF_001412225.1), proteins

Protein - Nicrophorus vespilloides Official Gene Set v1.0 proteins (Cunningham et al. 2015 Genome Biology and Evolution)

Nylanderia fulva

Protein

Protein - Nylanderia fulva NCBI Annotation release 100, translated CDS

Protein - nylful_OGSv1.1, translated CDS

Odontomachus brunneus

Protein

Protein - Odontomachus brunneus NCBI Annotation Release 100, translated CDS

Oncopeltus fasciatus

Protein

Protein - Oncopeltus fasciatus OGSv1.2, peptides

Onthophagus taurus

Protein

Protein - Onthophagus taurus NCBI Annotation release 100, translated CDS

Ornithodoros turicata

Protein

Protein - Ornithodoros turicata NCBI Annotation release GCF_037126465.1-RS_2024_04, translated CDS

Orussus abietinus

Protein

Protein - Orussus abietinus NCBI Annotation release 101, translated CDS

Protein - Orussus abietinus oruabi OGSv1.2, translated CDS

Osmia lignaria

Protein

Protein - Osmia lignaria NCBI Annotation Release 100, translated CDS

Pachypsylla venusta

Protein

Protein - Pachypsylla venusta Maker proteins v0.5.3 (BCM)

Parasteatoda tepidariorum

Protein

Protein - Parasteatoda tepidariorum Maker proteins v0.5.3 (BCM)

Protein - Augustus_set_v3.0_proteins

Pectinophora gossypiella

Protein

Protein - Pectinophora gossypiella NCBI Annotation release 100, translated CDS

Peregrinus maidis

Protein

Protein - Peregrinus maidis annotations v2023, translated CDS

Photinus pyralis

Protein

Protein - Photinus pyralis NCBI Annotation release 100, translated CDS

Plodia interpunctella

Protein

Protein - Plodia interpunctella NCBI Annotation release GCF_027563975.2-RS_2024_04, translated CDS

Rhagoletis zephyria

Protein

Protein - Rhagoletis zephyria Annotation Release 100 (GCF_001687245.1), proteins

Rhipicephalus microplus

Protein

Protein - Rhipicephalus microplus NCBI Annotation release 100, translated CDS

Schistocerca americana

Protein

Protein - Schistocerca americana NCBI Annotation release 100, translated CDS

Schistocerca cancellata

Protein

Protein - GCF_023864275.1_iqSchCanc2.1_protein.faa

Schistocerca gregaria

Protein

Protein - Schistocerca gregaria NCBI Annotation release 100, translated CDS

Schistocerca nitens

Protein

Protein - Schistocerca nitens NCBI Annotation release 100, translated CDS

Schistocerca piceifrons

Protein

Protein - Schistocerca piceifrons NCBI Annotation release 100, translated CDS

Schistocerca serialis

Protein

Protein - Schistocerca serialis NCBI Annotation release 100, translated CDS

Tigriopus californicus

Protein

Protein - Tigriopus californicus NCBI Annotation release GCF_007210705.1-RS_2023_08, translated CDS

Protein - Tigriopus californicus OGSv1.1, translated CDS

Tribolium castaneum

Protein

Protein - Tribolium castaneum NCBI Annotation release GCF_031307605.1-RS_2024_04, translated CDS

Protein - Tribolium castaneum OGSv3.1, translated CDS

Tribolium madens

Protein

Protein - Tribolium madens NCBI Annotation release 100, translated CDS

Trichogramma pretiosum

Protein

Protein - Trichogramma pretiosum NCBI Annotation release 101, translated CDS

Vanessa tameamea

Protein

Protein - Vanessa tameamea NCBI Annotation release GCF_037043105.1-RS_2024_03, translated CDS

Varroa destructor

Protein

Protein - Varroa destructor NCBI Annotation release 100, translated CDS

Varroa jacobsoni

Protein

Protein - Varroa jacobsoni NCBI Annotation release 100, translated CDS

Venturia canescens

Protein

Protein - Venturia canescens NCBI Annotation release 100, translated CDS

Vespa mandarinia

Protein

Protein - Vespa mandarinia NCBI Annotation release 100, translated CDS

Zeugodacus cucurbitae

Protein

Protein - Zeugodacus cucurbitae NCBI Annotation release GCF_028554725.1-RS_2023_03, translated CDS

Query Sequence / Mutliple sequence alignment

Enter sequence below in FASTA / IN MSA (format descriptions):

Or load it from disk (load sequence example) (load alignment example)

Program

phmmer hmmsearch

phmmer - Protein sequence vs. Ptotein sequence database

Cut-off

E-value Bit Score