benchamrk-proteinfamilies

Sample InterPro families (pre workflow) and test how well they can be reconstructed via nf-core/proteinfamilies (post workflow).

pre-proteinfamilies

During the pre workflow_mode, the InterPro hierarchy tree is parsed and sampled (different branches) for NCBIFAM, PANTHER, HAMAP and PFAM protein families. Their member amino acid sequences are compiled in a fasta file, along with unrelated sequences from UniProt-SwissProt.

A configuration file with the following paths must be provided:

interpo_hierarchy_file = '/path/to/interpro/ParentChildTreeFile.txt'
id_mapping_file        = '/path/to/interpro/interpro.xml.gz'
path_to_hamap          = '/path/to/hamap/hamap_alignments'
path_to_ncbifam        = '/path/to/ncbifam/hmm_PGAP'
path_to_panther        = '/path/to/panther/msa/PANTHER19.0_fasta'
path_to_pfam           = '/path/to/pfam/37.2/seed/alignments'
path_to_swissprot      = '/path/to/uniprot/fasta/uniprot_sprot_parsed.fasta'

Example versions and formats of the databases can be found here.

An example run command looks like this: nextflow run benchmark-proteinfamilies -c slurm_benchmark.config -profile singularity,slurm --workflow_mode pre -resume

nf-core/proteinfamilies

The generated output file named combined_decoy.fasta must be given as input to nf-core/proteinfamilies by placing its path in the samplesheet.csv input file.

An example run command looks like this: nextflow run proteinfamilies -c slurm.config -profile singularity,slurm --input samplesheet.csv --outdir /path/to/proteinfamilies/use-case/output_1 --clustering_tool cluster --cluster_size_threshold 3 --cluster_seq_identity 0.5 --hmmsearch_family_length_threshold 1 --remove_sequence_redundancy false --save_non_redundant_fams_fasta true -with-tower -resume

post-proteinfamilies

During the post workflow_mode, general statistics are caluclated regarding the coverage of the original families that was achieved by the generated families.

A configuration file with the following output paths from both pre mode of benchamrk-proteinfamilies and the nf-core/proteinfamilies run must be provided:

path_to_db_fasta             = '/path/to/benchmark_proteinfamilies/output/pre/families/sampled/combined_db.fasta'
path_to_decoys               = '/path/to/benchmark_proteinfamilies/output/pre/decoys/decoys.fasta'
path_to_sampled_metadata     = '/path/to/benchmark_proteinfamilies/output/pre/families/sampled/updated_sampled_metadata.csv'
path_to_sampled_fasta_folder = '/path/to/benchmark_proteinfamilies/output/pre/families/sampled/sampled_fasta'

path_to_alignments       = '/path/to/proteinfamilies/use-case/output_1/full_msa/filtered/hhsuite_reformat/use_case'
path_to_mmseqs_tsv       = '/path/to/proteinfamilies/use-case/output_1/mmseqs/initial_clustering/mmseqs_createtsv/use_case.tsv'
path_to_generated_fasta  = '/path/to/proteinfamilies/use-case/output_1/fasta/non_redundant_family_filtered/use_case'

An example run command looks like this: nextflow run benchmark-proteinfamilies -c slurm_benchmark.config -profile singularity,slurm --workflow_mode post -resume

Protein families database links and versions

Need to first download and decompress the protein family SEED alignments from the following databases, then update path parameters accordingly.

DB  ver link    last_update size
NCBIFAM 17.0    https://ftp.ncbi.nlm.nih.gov/hmm/current/hmm_PGAP.SEED.tgz  2024-12-16 10:56    67M
PANTHER 19.0    https://data.pantherdb.org/ftp/panther_library/current_release/PANTHER19.0_fasta.tgz    2024    461M
HAMAP   -   https://ftp.expasy.org/databases/hamap/hamap_alignments.tar.gz  2025-02-05 16:00    1.2G
PFAM    37.2    https://ftp.ebi.ac.uk/pub/databases/Pfam/releases/Pfam37.2/Pfam-A.seed.gz   2024-12-05 07:31    159M

NCBIFAM has two types of families; TIGRxxxxx and NFxxxxxx.

Linting

This repository uses pre-commit to enforce consistent formatting. Install it once after cloning:

pip install pre-commit
pre-commit install

Hooks run automatically on git commit. To run them manually against all files:

pre-commit run --all-files

The following hooks are configured:

• prettier — formats Nextflow, YAML, and Markdown files
• trailing-whitespace / end-of-file-fixer — general whitespace hygiene
• ruff — Python linting and formatting (bin/ scripts)

Example file formats

Example NF file: NF000005.4.SEED

>AAG34545.1/3-119
DQATPNLPSRDFDSTAAFYERLGFGIVFRDAGWMILQRGDLKLEFFAHPGLDPLASWFSCCLRLDDLAEFYRQCKSVGIQ
ETSSGYPRIHAPELQEWGGTMAALVDPDGTLLRLIQN
>WP_021018480.1/3-119
DQATPNLPSRDFDSTAAFYEKLGFRSVFRDSGWMILQRGDLILEFFAHPELDPLASWFSCCLRLDDLAGFYERCKSVGIQ
ETSRGYPRIHAPELQEWGGTMAALVDSDGTLLRLIQN
>SEP37262.1/3-119
DHATPNLPSRDFDATIAFYERLGFRAGFRDTGWMILEREGLVLEFFAYPELDPLTSWFSCCLRLDHLAEFYAQCKAAGIP
ESANGNPRLHAPKAQECGGIMAALIDLDGTLLRLIAN
>WP_000349358.1/2-118
DHATPNLPSRDFDATVAFYERLGFRLRFRDTGWMILERGGLVLEFLRHPELDPLTSWFSCCLRLDDLAGFYAHCEAAGIT
EATKGYPRLHAPQAQEWGGTMAALIDLDGTLLRLIAN
>WP_018641422.1/3-119
DLAIPNLPSRSFDRTQEFYRRLGFTLAYRDDEWMILNRGRVVLEFFAHPGLDPLASWFSCCLRLDELSEFYELCKSAGLE
EKGSGYPRLHPPEEQDGGGRMGALIDLDGTLLRLIQN

Example TIGR file: TIGR01051.1.SEED

# STOCKHOLM 1.0
SP|O83409|TOP1_TREPA/19-624             LVIVESPAKAQTIEKYLG.TQYVVRASMGHVIDLPKS.............................RLAIDIEHD..FQPEYITVRGRAQCLKELRTLSKQSLQVFLASDRDREGEAIAYHLAQSIQAYCDTP....IKRIVFNEITPHAIRAAIGHPVPIDTAKVNAQKARRVLDRLVGYHLCPLLWHKVKNGLSAGRVQSVALRLICEREVEVKRFVPEEYWTVEG.TFEKD......KKSFSALLILIQGKKAVFKS...................KQEATSAIGLFSQSEARVSQIRSFEKNVRPKQPFTTSTLQQCAANRLGFTSRKTMQVAQQLYEGVSLG.THRVGLITYMRTDSVRVSEAAVKEVRAWIATHFSDALPGTPN...RYAAKGK.SQDAHEAIRPT.YVAHTPERIKAHLTR...DQIRLYTLIWERFVASQMTDARVRSLTFEITA..G........PAVFSATETQVIEQGFYRVLKMLSPKDL......SKAVLPPTKEGEVVALHNVQSVQHFTQGPVRYTDASIVKMLEEKGIGRPSTYAPTISVLLDRYYVTRIQKQLMPTPLGKVISDLLTTYFHDVVDVSFTARMESKLDEVEEDKIKWNCVIADFYPAFSEKVST......VMKD..LNSMRGVFD...EKTDVVCSQCGD.TMVKKLGRFG..FFLACG.....KFP...ECRNTQPVP
SP|P46799|TOP1_THEMA/8-587              YIVVESPAKAKTIKSILG.NEYEVFASMGHIIDLPKS.............................KFGVDLEKD..FEPEFAVIKGKEKVVEKLKDLAKK.GELLIASDMDREGEAIAWHIARVTNTLGRK......NRIVFSEITPRVIREAVKNPREIDMKKVRAQLARRILDRIVGYSLSPVLWRNFKSNLSAGRVQSATLKLVCDREREILRFVPKKYHRIT..............VNFDGLTAEIDVKEKKF......................FDAETLKEIQSIDELVVEEKKVSVKKFAPPEPFKTSTLQQEAYSKLGFSVSKTMMIAQQLYEGVETK.DGHIAFITYMRTDSTRVSDYAKEEARNLITEVFGEEYVGSKR..ERRKSNAK.IQDAHEAIRPT.NVFMTPEEAGKYLNS...DQKKLYELIWKRFLASQMKPSQYEETRFVLRTKDG........KYRFKGTVLKKIFDGYEKVWKTER..........NTGEFP.FEEGESVKPVVVKIEEQETKPKPRYTEGSLVKEMERLGIGRPSTYASTIKLLLNRGYIKKIRGYLYPTIVGSVVMDYLEKKYSDVVSVSFTAEMEKDLDEVEQGKKTDKIVLREFYESFSSVFD..............RNDRIVVD...FPTNQKCS.CGK.EMRLSFGKYG..FYLKC............ECGKTRSVK
SP|P39814|TOP1_BACSU/5-612              LVIVESPAKAKTIERYLG.KKYKVKASMGHVRDLPKS.............................QMGVDIEQN..FEPKYITIRGKGPVLKELKTAAKKAKKVYLAADPDREGEAIAWHLAHSLDLDLNS.....DCRVVFNEITKDAIKESFKHPRMINMDLVDAQQARRILDRLVGYKISPILWKKVKKGLSAGRVQSVALRLIIDREKEINDFKPEEYWTIDG.TFLKG......QETFEASFFGKNGKKLPLNS...................EADVKEILSQLKGNQYTVEKVTKKERKRNPALPFTTSTLQQEAARKLNFRAKKTMMIAQQLYEGIDLGREGTVGLITYMRTDSTRISNTAVDEAAAFIDQTYGKEFLGGKR..KPAKKNEN.AQDAHEAIRPT.SVLRKPSELKAVLGR...DQMRLYKLIWERFVASQMAPAVLDTMSVDLTN..N........GLTFRANGSKVKFSGFMKVYVEGKDDQME....EKDRMLPDLQEGDTVLSKDIEPEQHFTQPPPRYTEARLVKTLEERGIGRPSTYAPTLDTIQRRGYVALDNKRFVPTELGQIVLDLIMEFFPEIINVEFTAKMERDLDHVEEGNTEWVKIIDNFYTDFEKRVKK......AES...EMKEVEIEP...EYAGEDCELCSS.PMVYKMGRYG..KFLACS.....NFP...DCRNTKPIV
SP|P06612|TOP1_ECOLI/5-637              LVIVESPAKAKTINKYLG.SDYVVKSSVGHIRDLPTSGSAAKKSADSTSTKTAKKPKKDERGALVNRMGVDPWHN..WEAHYEVLPGKEKVVSELKQLAEKADHIYLATDLDREGEAIAWHLREVIGGDDAR.....YSRVVFNEITKNAIRQAFNKPGELNIDRVNAQQARRFMDRVVGYMVSPLLWKKIARGLSAGRVQSVAVRLVVEREREIKAFVPEEFWEVDASTTTPS......GEALALQVTHQNDKPFRPVN...................KEQTQAAVSLLEKARYSVLEREDKPTTSKPGAPFITSTLQQAASTRLGFGVKKTMMMAQRLYE.........AGYITYMRTDSTNLSQDAVNMVRGYISDNFGKKYLPESP..NQYASKEN.SQEAHEAIRPS.DVNVMAESLKD.MEA...DAQKLYQLIWRQFVACQMTPAKYDSTTLTVGA..G........DFRLKARGRILRFDGWTKVMPALRKGD.......EDRILPAVNKGDALTLVELTPAQHFTKPPARFSEASLVKELEKRGIGRPSTYASIISTIQDRGYVRVENRRFYAEKMGEIVTDRLEENFRELMNYDFTAQMENSLDQVANHEAEWKAVLDHFFSDFTQQLDK......AEKDPEEGGMRPNQM...VLTSIDCPTCGR.KMGIRTASTG..VFLGCSG...YALPPKERCKTTINLV
OMNI|DR1374/48-701                      LVIVESPAKAKTIEKYLG.QGYAVESSVGHIRDLPRSAADIPEKYKG...........QA....WARLGLDVEHD..FQPLYVVSPEKKQKVAQLRKLAAEADEIILATDDDREGESIAWHLYQELKPKVPV......KRMVFHEITREAIQAAIAAPRQIDRNLVEAQEARRAVDRLYGYEVSPVLWRKVAPKLSAGRVQSVATRMLVERERERMRFVAATWWDVVVTAQALT..AQAGEQTFPARLTEVQGERLAAGKDFDPLTGQLRPGAGVRLLGEAEALAISEGLKGQTLKVLTAEEKPFTSRPPAPFITSTLQQEGSRKLRMSAQTTMRTAQRLYEG.........GYITYMRTDSTNLSSEAVNAARGQVKDMYGAPYLSPQP..RVYAKKSKNAQEAHEAIRPAGSTFRTPEQLRGELSG...DEWRLYDLIWKRTVASQMSDARGRSLRVRLGGQTASGQTADSVPVVLNASGRTIDFPGFLRAYVEGSDDPAA.ALEDRDTPLPPLKXGDAVRAQDVKAEDHETQPPARYTEASLVQALEGAGIGRPSTYASILGTIQDRGYALKKGTALVPSWTAFATSALLEHHFGTLVDYDFTAKMEEDLDEIAGGREHRVPYLRRFYLGEEG.......EGMALKPLIERQMGEIDARGIATIKVP.KLEGS.GIEVRVGRYG..PYMQR......GE...DKANLPEGMT
SP|Q59567|TOP1_MYCTU/20-689             LVIVESPTKARKLASYLG.SGYIVESSRGHIRDLPRAASDVPAKYKS...........QP....WARLGVNVDAD..FEPLYIISPEKRSTVSELRGLLKDVDELYLATDGDREGEAIAWHLLETLKPRIPV......KRMVFHEITEPAIRAAAEHPRDLDIDLVDAQETRRILDRLYGYEVSPVLWKKVAPKLSAGRVQSVATRIIVARERDRMAFRSAAYWDILAKLDASVSDPDAAPPTFSARLTAVAGRRVATGRDFDSLG.TLRKGDEVIVLDEGSATALAAGLDGTQLTVASAEEKPYARRPYPPFMTSTLQQEASRKLRFSAERTMSIAQRLYEN.........GYITYMRTDSTTLSESAINAARTQARQLYGDEYVAPAP..RQYTRKVKNAQEAHEAIRPAGETFATPDAVRRELDGPNIDDFRLYELIWQRTVASQMADARGMTLSLRITGMSG......HQEVVFSATGRTLTFPGFLKAYVETVDELVGGEADDAERRLPHLTPGQRLDIVELTPDGHATNPPARYTEASLVKALEELGIGRPSTYSSIIKTIQDRGYVHKKGSALVPSWVAFAVTGLLEQHFGRLVDYDFTAAMEDELDEIAAGNERRTNWLNNFYFGGDHGVPDSVARSGGLKKLVGINLEGIDAREVNSIKLFDDTHGR.PIYVRVGKNG..PYLERLVAGDTGEPTPQRANLSDSIT
SP|P73810|TOP1_SYNY3/4-637              LVIVESPTKARTIRNYLP.QDYRVEASMGHVRDLPASAEEVPAAYKD...........KS....WANLGVNVEDH..FSPLYVIPKSKKKVVKELQTALKNADEVILATDEDREGESISWHLLQLLQPKVPI......KRMVFHEITQEAIRSALENCRDIDENLVHAQETRRILDRLVGYTLSPLLWKKIAWGLSAGRVQSVAVRLIVQRERARRAFKTAGYWDLKAELEQNK...NP....FQAKLMTLGGTKLANGSDFDPNTGALLPDKQVVVLDEAQAIALKERLTGKPWAVVNTEEKPGVRKPSPPFTTSTLQQEANRKLGISARDTMRVAQKLYEE.........GYITYMRTDSVHLSDQAVTAARNCVQQMYGKEYLSPQP..KQYTTKSKGAQEAHEAIRPAGTEFRIPNQTG..LKD...RELALYELIWKRTVACQMADARITQLSVLLKVEDA..........EFRAAGKRIDFPGYFRAYVEGSDDPDA.ALENQEVILPPLKVGDRPNCREIDTVGHETQPPARYTEASLVKTLESEGVGRPSTYASIIGTIIDRGYVQMRSKALTPTFTAFAVVSLLESHFPDLVDTGFTSRMEQKLDEIAIGKTQWLPYLQGFFLGESG...........LENQVKVRQDQIDP....AIAKAIELENL.AAKVKIGKFG..PYIEIP...Q.GE.EIITASIPQDLT
SP|Q9ZDK2|TOP1_RICPR/3-634              LVIVESPAKAKTINKYLG.DEFKVIASFGHIRDLPSK.............................KGSVLPDKN..FLMEYDISDKAGKYVDAIVKEARKAEVVYLATDPDREGESISWHVAEVIKEKNKVESDDFFKRVAFNEITKKAIMNAVANPRKLDTNLVNAQQARRALDYLVGFTLSPLLWRKLPGCKSAGRVQSVALRLICDREDEIERFKSEEYWDISLKMQNSN......NDLFTAKLTHVNDQKLKKFS................IINEKEAKDLTQKLKLQKFYVEKIEKKQQKRQPQPPFITSSLQQEAARKLGFSAKKTMQIAQKLYEGVDIG.KETIGLITYMRTDGVTLSNDAIADIRKLIDKNYGNQYLPIKP..RIYQSKVKNAQEAHEAIRPT.NITYTPDSLKQKLEK...DYYKLYELIWHRTIACQMENVIMDLVIANLASENK........EYLAKANGSIIAFDGFYKVYRESLDDEDE....EDNKMLPPLKEQEHIKTKEVIPNKHFTEPPPRYSEASLVKKLEELGIGRPSTYASILSVLQDRKYVALEKKRFIPEELGRLVTVFLVGFFKKYVEYDFTAGLENELDEIAAGKLEWKTALNNFWRGFNHNIESVNEQKITEIINYLQKALDYHLFGEDKESKVCPSCKTGQLSLKLGKFG..AFLACS.....NYP...ECTFKKSIV
SP|P55991|TOP1_HELPY/4-605              LIIVESPAKAKTIKNFLD.KNYEVIASKGHVRDLSKF.............................ALGIKIDETG.FTPNYVVDKDHKELVKQIIELSKKASITYIATDEDREGEAIGYHVACLIGGKLES.....YPRIVFHEITQNAILNALKTPRKIDMSKVNAQQARRFLDRIVGFKLSSLIASKITKGLSAGRVQSAALKLVIDKEREIKAFKPLTYFTLDAYFES..........HLEAQLISYKGNKLKAQELID................EKKAQEIKNELEKESYAISSIVKKSKKSPTPPPFMTSTLQQSASSLLGFSPTKTMSIAQKLYEGVATP.QGVMGVITYMRTDSLNIAKEALEEARNKILKDYGKDYLPPKA..KVYSSKNKNAQEAHEAIRPT.SIILEPNALKDYLKP...EELRLYTLIYKRFLASQMQDALFESQSVVVACEKG..........EFKASGRKLLFDGYYKILGN..DD........KDKLLPNLKENDPIKLEKLESNAHVTEPPARYSEASLIKVLESLGIGRPSTYAPTISLLQNRDYIKVEKKQISALESAFKVIEILEKHFEEIVDSKFSASLEEELDNIAQNKADYQQVLKDFYYPFMDKIEA.............GKKNIISQKVHEKTGQSCPKCGG.ELVKKNSRYG..EFIACN.....NYP...KCKYVKQTE
SP|P47368|TOP1_MYCGE/5-653              LVVIESPNKVKTLKQYLPSDEFEIVSTVGHIREMVYKNFGFDEN...................TYTPIWEDWTKNKQKNPKQKHLLSKFEIIKSIKAKASDAQNIFLASDPDREGEAISWHVYDLLDQKDKAK....CKRITFNEITKKAVVDALKQPRNIDLNWVESQFARQILDRMIGFRLSRLLN.SYLQAKSAGRVQSVALRFLEEREKEIAKFVPRFWWTVDVLLNKENNQKVVCANKSIPLVLREINPELSASLKLDFEAAENVSG..IDFLNEASATRFANQLTGEYEVYFIDEPKIYYSSPNPVYTTASLQKDAINKLGWSSKKVTMVAQRLYEGISVN.GKQTALISYPRTDSIRISNQFQSECEKYIEKEFGSHYLADKNKLKRHKKDEKIIQDAHEGIHPT.YITITPNDLKNGVKR...DEFLLYRLIWIRTVASLMADAKTSRTIVRFINQKN..........KFYTSSKSLLFDGYQRLYEEIKPNTKD....ELYIDLSKLKIGDKFSFEKISVNEHKTNPPPRYTQASLIEELEKSNIGRPSTYNTMASVNLERGYANLVNRFFYITELGEKVNNELSKHFGNVINKEFTKKMEKSLDEIAENKVNYQEFLKQFWTNFKSDVK............LAENSIQKVKKEKELVERDCPKCNQ.PLVYRYTKRGNEKFVGCS.....DFP...KCKYSEFSN
//

Example PANTHER file: PTHR10059.fasta

>BOVIN|Ensembl=ENSBTAG00000001570|UniProtKB=P11052
MWLQNLLLLGTVVCSFSAPTRPPNTATRPWQHVDAIKEALSLLNHSSDTDAVMNDTEVVS
EKFDSQEPTCLQTRLKLYKNGLQGSLTSLMGSLTMMATHYEKHCPPTPETSCGTQFISFK
NFKEDLKEFLFIIPFDCWEPAQK
>PIG|Ensembl=ENSSSCG00000023737.3|UniProtKB=I3L8Q3
MWLQNLLLLGTVVCSISAPTRPPSPVTRPWQHVDAIKEALSLLNNSNDTAAVMNETVDIV
CEMFDPQEPTCVQTRLNLYKQGLRGSLTRLKSPLTLLAKHYEQHCPLTEETSCETQSITF
KSFKDSLNKFLFTIPFDCWGPVKK
>PANTR|Ensembl=ENSPTRG00000017212.2|UniProtKB=H2QRG1
MWLQSLLLLGTVACSISAPARSPSPSTQPWEHVNAIQEARRLLNLSRDTAAEMNETVEVV
SEMFDLQEPTCLQTRLELYKQGLRGSLTKLKGPLTMMASHYKQHCPPTPETSCATQIITF
ESFKENLKDFLLVIPLDCWEPVQE
>FELCA|Ensembl=ENSFCAG00000003852.5|UniProtKB=A0A0A0MPY1
MWLQNLLFLGTVVCSISAPTSSPSSVTRPWQHVDAIKEALSLLNNSSEITAVMNEAVEVV
SEMFDPEEPKCLQTHLKLYEQGLRGSLISLKEPLRMMANHYKQHCPLTPETPCETQTITF
KNFKENLKDFLFNIPFDCWKPV
>CANLF|Ensembl=ENSCAFG00845009774.1|UniProtKB=A0A8I3ND87
MWLQNLLFLGTVVCSISAPTRSPTLVTRPSQHVDAIQEALSLLNNSNDVTAVMNKAVKVV
SEVFDPEGPTCLETRLQLYKEGLQGSLTSLKNPLTMMANHYKQHCPPTPESPCATQNINF
KSFKENLKDFLFNIPFDCWGKTSQELSTPPRPVVVFCIGTEQ
>PIG|Ensembl=ENSSSCG00015030234|UniProtKB=Q29118
MWLQNLLLLGTVVCSISAPTRPPSPVTRPWQHVDAIKEALSLLNNSNDTAAVMNETVDVV
CEMFDPQEPTCVQTRLNLYKQGLRGSLTRLKSPLTLLAKHYEQHCPLTEETSCETQSITF
KSFKDSLNKFLFTIPFDCWGPVKK
>RAT|RGD=621065|UniProtKB=P48750
MWLQNLLFLGIVVYSFSAPTRSPNPVTRPWKHVDAIKEALSLLNDMRALENEKNEDVDII
SNEFSIQRPTCVQTRLKLYKQGLRGNLTKLNGALTMIASHYQTNCPPTPETDCEIEVTTF
EDFIKNLKGFLFDIPFDCWKPVQK
>MACMU|Ensembl=ENSMMUG00000016915.4|UniProtKB=Q9GL44
MWLQGLLLLGTVACSISAPARSPSPGTQPWEHVNAIQEARRLLNLSRDTAAEMNKTVEVV
SEMFDLQEPSCLQTRLELYKQGLQGSLTKLKGPLTMMASHYKQHCPPTPETSCATQIITF
QSFKENLKDFLLVIPFDCWEPVQE
>MOUSE|MGI=MGI=1339752|UniProtKB=P01587
MWLQNLLFLGIVVYSLSAPTRSPITVTRPWKHVEAIKEALNLLDDMPVTLNEEVEVVSNE
FSFKKLTCVQTRLKIFEQGLRGNFTKLKGALNMTASYYQTYCPPTPETDCETQVTTYADF
IDSLKTFLTDIPFECKKPGQK
>HUMAN|HGNC=2434|UniProtKB=P04141
MWLQSLLLLGTVACSISAPARSPSPSTQPWEHVNAIQEARRLLNLSRDTAAEMNETVEVI
SEMFDLQEPTCLQTRLELYKQGLRGSLTKLKGPLTMMASHYKQHCPPTPETSCATQIITF
ESFKENLKDFLLVIPFDCWEPVQE
>GORGO|Ensembl=ENSGGOG00000001046.3|UniProtKB=G3QFF8
MWLQSLLLLGTVACSISAPARSPSPSTQPWEHVNAIQEARRLLNLSRDTAAEMNGTVEVI
SEMFDLQEPTCLQTRLELYKQGLQGSLTKLKGPLTMMASHYKQHCPPTPETSCATQIITF
ESFKENLKDFLLVIPFDCWEPVQE
>FELCA|Gene=CSF2|UniProtKB=O62757
MWLQNLLFLNTVVCSISAPTSSPSSVTRPWQHVDAMKEALSLLNNSSEITAVMNETVEVV
SEMFDPEEPKCLQTHLKLYEQGLRGSLISLKEPLRMMANHYKQHCPLTPETPCETQTITF
KNFKEKLKDFLFNNPFDCWGPDQK
>CANLF|Ensembl=ENSCAFG00805013973|UniProtKB=P48749
MWLQNLLFLGTVVCSISAPTRSPTLVTRPSQHVDAIQEALSLLNNSNDVTAVMNKAVKVV
SEVFDPEGPTCLETRLQLYKEGLQGSLTSLKNPLTMMANHYKQHCPPTPESPCATQNINF
KSFKENLKDFLFNIPFDCWKPVKK
>HORSE|Ensembl=ENSECAG00000009678.3|UniProtKB=B1AB91
MWLQNLLLLGTVVYSMPAPTRQPSPVTRPWQHVDAIKEALSLLNNSSDTAAIMNETVEVV
SETFDAEELTCLQTRLKLYKQGLRGSLIKLEGPLTMMASHYKQHCPPTLETSCATQMITF
KSFKKNLKDFLFEIPFDCWSQPRSKAGLPARS

Example HAMAP file: MF_00264.msa

>A0A0S3QRG7_THET7 L=1  103.017  11200 pos.        1 -     230 [   21,    -4] T|A0A0S3QRG7|A0A0S3QRG7_THET7
--------------------MSVVELREIQALNTLVFETLGQPEKEREFKFKTLKRWGLD
LILGKKNGSETYFVSEYGKRHKGDVYTEDGVEYEVSEILEELPSNKKLFAHIEMKDGRAY
LVGQLREGDD.NIEILRLPAASLLLAYFKKHRLHHLIEALRNVGTATELVKQRG-QEGKP
YPFEQLPNVARIFLREAKKVEKE-AGFGRVALAYFGENkDGDARFRVSWLLPTIALFELD
IAEKADKILAAFK---
>C5A445_THEGJ L=1  134.298  14670 pos.        1 -     222 [   30,    -4] T|C5A445|C5A445_THEGJ
-----------------------------MLEGYYIVENTGVVPAERRFKFKDLKAWGYD
LHLGTIDGKEAYFVSRTGTHEEGETYTQDGREYHITETQREIPKNARLLARIVIERGQPY
LEFWLEAEEA.NYPLAKEDPRLILHRFWTAKKFNQLEKHVGSVGLTTDFFKDRVFVKSLP
LPFEEYPPKVRRVLREVRDVHRDLTGFGRFVFQYYGEE.DKTHNYRLWWLLPTIHLFDIE
VSNEVDKILAMLD---
>W0I238_9EURY L=1  134.415  14683 pos.        1 -     222 [   30,    -4] T|W0I238|W0I238_9EURY
-----------------------------MLEGYYIIENSGVVPAERRFKFKDLKAWGYD
LHLGTIEGERAYFVSGAGEREEGETYTVKGKEYHITETQQEIPSNARLLAKIVIEKGQPY
LVFWLEEEEQ.TFPLAKEDPRIILRRFWEAKKFKQLLKHVNSVGLTTDFYKDNVFTRSIP
LPYEEYPPKVRRVLREVRDIHRDLTGFGRFVFQYYGEE.DKMHNYRLWWLLPTIYLFDVE
IANEIDKILGMLD---
>Y1314_PYRHO L=1  143.664  15709 pos.        1 -     225 [   27,    -4] S|O59052|Y1314_PYRHO
--------------------------MIKMLEGYYIIENPGVVPAERRFRMKDLKAWGYD
LHLGTIEGERAYFISKTGERHEGETYIFKGKEYHVSRTQKEIPENARLLARIIIERGNPY
LEVWLEEEDV.KFPLTKEDPRIILKRIWEKEKLNQLLKHVRAVGLTTDFYKDNVFTQGIP
LPYEEYPPKVRRVLREVKDIHRDLTGFGRFVFQYFGEV.DKMHNYRLYWTLPTLHLFDID
IANEVDKVLGMLD---
>Y1463_METJA L=1  114.691  12495 pos.        1 -     233 [   22,    -1] S|Q58858|Y1463_METJA
---------------------MVVDAKEVEMINTLVFETLGNPEKEREFKLKSLKRWGFD
LIFGKVDGKETYFTVELDERKAGDKFSKDGKEYEVIEVLQELPKNTELYAHIEMEMGKAY
IVCQLRDEDGkNTEVLRVPAATLLLAFLKKNKLANIIKAIKNVGISLELSMQNG-VGGKP
LSYEELPNVARRFIRSARKVEKE-TGFGRLSFAYYGETkDGEPRYRFSWLLPTIALFDLD
IAKKVEQTLGILKVSE
>Y1488_PYRFU L=1  142.104  15536 pos.        1 -     222 [   30,    -4] S|Q8U0U4|Y1488_PYRFU
-----------------------------MLEGYYIIENPGVVPSERRFRMKDLKAWGYD
LHLGTIEGERAYFVSRTGEREEGETYSLQGKTYHIEKTEKEIPENARLLARIVIERGQPY
LEFWLEEEDT.VYPLAKEDPRIILKRLWEKEKLNQLLKHVRAVGLTTDFYKDTVFIKSIP
LPYEEYPPKVRRVLREVRDIHRDIMGFGRFVFQYFGEE.NKTHNYRLHWTLPTLHLFDVE
IANEIDKVLGMLD---
>Y2294_THEKO L=1  139.778  15278 pos.        1 -     222 [   30,    -4] S|Q5JDC5|Y2294_THEKO
-----------------------------MLEGYYIVENTGVVPAERRFKFKDLKAWGYD
LHLGTIDGREAYFVSKAGTREEGETYTEGGKEYHISETQKEIPKNARLLARIVIEKGQPY
LEFWLDTEDG.NFPLAKEDPRLILHRFWTEKKFNQLEKHVGSVGLTTDFFKDRVFVKSIP
LPYEEYPPKVRRVLREVRDVHRDLTGFGRFVFQYFGEE.DKTHQYRLWWLLPTIHLFDVE
VSNEVDKILAMLD---
>Y756_AQUAE L=1  109.111  11876 pos.        1 -     229 [   21,    -4] S|O66958|Y756_AQUAE
--------------------MDKKELVEKIALNTLVFETLGQPEKEREFTIQDLRRWGFD
LILGKKNGVRTFFASQAG-REVGDKWEEGGATYEIEEILLELPENKKLFAHIETSEGVAY
IVAELREGKE.NLEILRTPAPTLLMAFFKKHRLHELANNLKSVGVITEFYKQRG-RESLP
LPYKKLPLVARDFLERAKKVEKM-AGFGRVALAYFGKTrEKDNRFRVSWLLPTIALFDID
ISEKANTALEEFK---
>Y832_PYRAB L=1  143.456  15686 pos.        1 -     222 [   30,    -4] S|Q9V0F7|Y832_PYRAB
-----------------------------MMEGYYIIENPGVVPAERRFRMKDLKAWGYD
LHLGTIEGERAYFVSKVGERREGEKYQVGGKEYYIEETQKDIPGNARLLARIVIERGNPY
LEFWLEEEDT.KFPLAKEDPRIILKRIWEKEKLNQLLKHVRAIGLTTDFYKDNVFIKSIP
LPYEEYPPKVRRVLREVRDIHRDLTGFGRFVFQYFGEV.EKAHNYRLHWTLPTLHLFDVD
IANEVDKILGMLD---

PFAM requires some preprocessing to break the single STOCKHOLM formatted SEED file into multiple ones.

Example PFAM file: PF00093.sto

# STOCKHOLM 1.0
#=GF ID   VWC
#=GF AC   PF00093.24
#=GF DE   von Willebrand factor type C domain
#=GF PI   vwc;
#=GF AU   Sonnhammer ELL;0000-0002-9015-5588
#=GF SE   Published_alignment
#=GF GA   27.60 27.60;
#=GF TC   27.60 27.60;
#=GF NC   27.50 27.50;
#=GF BM   hmmbuild  HMM.ann SEED.ann
#=GF SM   hmmsearch --cpu 4 -E 1000 -Z 81514348 HMM pfamseq
#=GF TP   Domain
#=GF WK   Von_Willebrand_factor_type_C_domain
#=GF CL   CL0451
#=GF RN   [1]
#=GF RM   7687569
#=GF RT   The modular architecture of a new family of growth regulators
#=GF RT   related to connective tissue growth factor.
#=GF RA   Bork P;
#=GF RL   FEBS Lett 1993;327:125-130.
#=GF DR   INTERPRO; IPR001007;
#=GF DR   SO; 0000417; polypeptide_domain;
#=GF CC   The high cutoff was used to prevent overlap with Pfam:PF00094.
#=GF SQ   19
#=GS CO5A2_HUMAN/41-96         AC P05997.3
#=GS CO3A1_MOUSE/33-89         AC P08121.4
#=GS CO2A1_MOUSE/34-88         AC P28481.2
#=GS CO1A1_HUMAN/40-95         AC P02452.6
#=GS CO1A1_CHICK/33-88         AC P02457.3
#=GS A0A6I8RQ44_XENTR/324-378  AC A0A6I8RQ44.2
#=GS TSP1_HUMAN/318-372        AC P07996.2
#=GS TSP2_MOUSE/320-374        AC Q03350.2
#=GS TSP2_CHICK/326-380        AC P35440.1
#=GS SOG_DROME/941-1019        AC Q24025.1
#=GS SOG_DROME/832-898         AC Q24025.1
#=GS SOG_DROME/102-174         AC Q24025.1
#=GS CCN1_CHICK/100-163        AC P19336.1
#=GS CCN3_CHICK/106-169        AC P28686.1
#=GS CCN2_HUMAN/103-166        AC P29279.2
#=GS VWF_HUMAN/2257-2325       AC P04275.4
#=GS VWF_HUMAN/2431-2494       AC P04275.4
#=GS VWF_HUMAN/2582-2644       AC P04275.4
#=GS SOG_DROME/744-803         AC Q24025.1
CO5A2_HUMAN/41-96                    CT.QNGQMYLNRDIWKPAP........CQ.ICVCDN........GAILCDKIE..CQD.....VLDCADP................VTPPGECCP..VC
CO3A1_MOUSE/33-89                    CS.HLGQSYESRDVWKPEP........CQ.ICVCDS........GSVLCDDII..CDEE....PLDCPNP................EIPFGECCA..IC
CO2A1_MOUSE/34-88                    CL.QNGQRYKDKDVWKPSS........CR.ICVCDT........GNVLCDDII..CED......PDCLNP................EIPFGECCP..IC
CO1A1_HUMAN/40-95                    CV.QNGLRYHDRDVWKPEP........CR.ICVCDN........GKVLCDDVI..CDE.....TKNCPGA................EVPEGECCP..VC
CO1A1_CHICK/33-88                    CV.QDGLTYNDKDVWKPEP........CQ.ICVCDS........GNILCDEVI..CED.....TSDCPNA................EIPFGECCP..IC
A0A6I8RQ44_XENTR/324-378             CL.HNGVLHKNRDEWTVDS........CT.ECTCQN........SATICRKVS..CPL......MPCTNA................TIPDGECCP..RC
TSP1_HUMAN/318-372                   CY.HNGVQYRNNEEWTVDS........CT.ECHCQN........SVTICKKVS..CPI......MPCSNAT............VP....DGECCP..RC
TSP2_MOUSE/320-374                   CV.QEGRIFAENETWVVDS........CT.TCTCKK........FKTVCHQIT..CSP......ATCANP................SFVEGECCP..SC
TSP2_CHICK/326-380                   CW.QDGRVFADSESWIVDS........CT.KCTCQD........SKIVCHQIT..CPP......VSCADP.............SF...IEGECCP..VC
SOG_DROME/941-1019                   CK.VVNKVYENGQEWHPILMSH.GEQKCI.KCRCKD........SKVNCDRKR..CSR......STCQQQTRVTSKRRLFEKPDAAAPAIDECCS.TQC
SOG_DROME/832-898                    CR.LGEQFHPAGASWHPFLPPN.GFDTCT.TCSCDPL......TLEIRCPRLV..CPP......LQCSEK.............LAYRPDKKACCK..IC
SOG_DROME/102-174                    CQ.FGKVLRELGSTWYADLGPPFGVMYCI.KCECVAIPKKRRIVARVQCRNIKNECPP......AKCDDP................ISLPGKCCK..TC
CCN1_CHICK/100-163                   CE.YNSKIYQNGESFQPN.........CKHQCTCID........GAVGCIPL...CPQELSLPNLGCPSP..............RLVKVPGQCCEEWVC
CCN3_CHICK/106-169                   CV.FDGMIYRNGETFQPS.........CKYQCTCRD........GQIGCLPR...CNLGLLLPGPDCPFP..............RKIEVPGECCEKWVC
CCN2_HUMAN/103-166                   CI.FGGTVYRSGESFQSS.........CKYQCTCLD........GAVGCMPL...CSMDVRLPSPDCPFP..............RRVKLPGKCCEEWVC
VWF_HUMAN/2257-2325                  CIGEDGVQHQFLEAWVPDHQ......PCQ.ICTCLS.......GRKVNCTTQP..CPTAKAPTCGLCEVA..............RLRQNADQCCPEYEC
VWF_HUMAN/2431-2494                  CV.HRSTIYPVGQFWEEG.........CD.VCTCTDMEDAVMGLRVAQCSQKP..CE.......DSCRSG.............FTYVLHEGECCG..RC
VWF_HUMAN/2582-2644                  CM.LNGTVIGPGKTVMIDV........CT.TCRCMVQVG.VISGFKLECRKTT..C........NPCPLG.............YKEENNTGECCG..RC
SOG_DROME/744-803                    CF.HSGRFYNESEQWRSAQD......SCQ.MCACLR........GQSSCEVIK..CPA......LKCKST.............EQLLQRDGECCP..SC
#=GC seq_cons                        Ch.psGphYpss-sWpss.........Cp.hCsCps........uplhCcpl...Cs.......hsCsss..................s.GECCs..hC
//