anvi-get-sequences-for-hmm-hits

Get sequences for HMM hits from many inputs.

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Authors

A. Murat Eren (Meren)
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Can consume

contigs-db profile-db external-genomes internal-genomes hmm-source hmm-hits

Can provide

genes-fasta concatenated-gene-alignment-fasta

Usage

This program can work with anvi’o contigs-db, external-genomes, or internal-genomes files to return sequences for HMM hits identified through the default anvi’o hmm-sources (such as the domain-specific single-copy core genes) or user-defined hmm-sources (such as HMMs for specific antibiotic resistance gene families or any other targets).

Using it with single-copy core genes in default anvi’o HMMs make it a very versatile tool for phylogenomics as the user can define specific sets of genes to be aligned and concatenated.

Learn available HMM sources

anvi-get-sequences-for-hmm-hits -c contigs-db \ --list-hmm-sources

AVAILABLE HMM SOURCES =============================================== * ‘Bacteria_71’ (type: singlecopy; num genes: 71) * ‘Archaea_76’ (type: singlecopy; num genes: 76) * ‘Protista_83’ (type: singlecopy; num genes: 83) * ‘Ribosomal_RNAs’ (type: Ribosomal_RNAs; num genes: 12)

Get all sequences in a given HMM source

anvi-get-sequences-for-hmm-hits -c contigs-db \ --hmm-source Bacteria_71 \ -o genes-fasta

Learn available genes in a given HMM source

Please note that the flag --list-available-gene-names will give you the list of genes in an HMM collection (for example, for Bacteria_71 in the following use case), and it will not give you the list of genes in your genomes or metagenomes that are matching to them. You can generate a table of HMMs across your genomes or metagenomes with another program, anvi-script-gen-hmm-hits-matrix-across-genomes.

anvi-get-sequences-for-hmm-hits -c contigs-db \ --hmm-source Bacteria_71 \ --list-available-gene-names

* Bacteria_71 [type: singlecopy]: ADK, AICARFT_IMPCHas, ATP-synt, ATP-synt_A, Chorismate_synt, EF_TS, Exonuc_VII_L, GrpE, Ham1p_like, IPPT, OSCP, PGK, Pept_tRNA_hydro, RBFA, RNA_pol_L, RNA_pol_Rpb6, RRF, RecO_C, Ribonuclease_P, Ribosom_S12_S23, Ribosomal_L1, Ribosomal_L13, Ribosomal_L14, Ribosomal_L16, Ribosomal_L17, Ribosomal_L18p, Ribosomal_L19, Ribosomal_L2, Ribosomal_L20, Ribosomal_L21p, Ribosomal_L22, Ribosomal_L23, Ribosomal_L27, Ribosomal_L27A, Ribosomal_L28, Ribosomal_L29, Ribosomal_L3, Ribosomal_L32p, Ribosomal_L35p, Ribosomal_L4, Ribosomal_L5, Ribosomal_L6, Ribosomal_L9_C, Ribosomal_S10, Ribosomal_S11, Ribosomal_S13, Ribosomal_S15, Ribosomal_S16, Ribosomal_S17, Ribosomal_S19, Ribosomal_S2, Ribosomal_S20p, Ribosomal_S3_C, Ribosomal_S6, Ribosomal_S7, Ribosomal_S8, Ribosomal_S9, RsfS, RuvX, SecE, SecG, SecY, SmpB, TsaE, UPF0054, YajC, eIF-1a, ribosomal_L24, tRNA-synt_1d, tRNA_m1G_MT, Adenylsucc_synt

Get sequences for some sequences in a given HMM source

anvi-get-sequences-for-hmm-hits -c contigs-db \ --hmm-source Bacteria_71 \ --gene-names Ribosomal_L27,Ribosomal_L28,Ribosomal_L3 \ -o genes-fasta

Get HMM hits in bins of a collection

anvi-get-sequences-for-hmm-hits -c contigs-db \ -p profile-db \ -C collection --hmm-source Bacteria_71 \ --gene-names Ribosomal_L27,Ribosomal_L28,Ribosomal_L3 \ -o genes-fasta

Get amino acid sequences for HMM hits

anvi-get-sequences-for-hmm-hits -c contigs-db \ -p profile-db \ -C collection --hmm-source Bacteria_71 \ --gene-names Ribosomal_L27,Ribosomal_L28,Ribosomal_L3 \ --get-aa-sequences \ -o genes-fasta

Get HMM hits independently aligned and concatenated

The resulting file can be used for phylogenomics analyses via anvi-gen-phylogenomic-tree or through more sophisticated tools for curating alignments and computing trees.

anvi-get-sequences-for-hmm-hits -c contigs-db \ -p profile-db \ -C collection --hmm-source Bacteria_71 \ --gene-names Ribosomal_L27,Ribosomal_L28,Ribosomal_L3 \ --get-aa-sequences \ --concatenate-genes \ --return-best-hit -o genes-fasta

Want to play?

You can play with this program using the anvi’o data pack for the infant gut data and by replacing the parameters above with appropriate ones in the following commands.

Download the latest version of the data from here:

doi:10.6084/m9.figshare.3502445

Unpack it:

tar -zxvf INFANTGUTTUTORIAL.tar.gz && cd INFANT-GUT-TUTORIAL

Import the collection merens:

anvi-import-collection additional-files/collections/merens.txt \ -p PROFILE.db \ -c CONTIGS.db \ -C merens

Then run the program to

Learn available HMM sources

anvi-get-sequences-for-hmm-hits -p PROFILE.db \ -c CONTIGS.db \ -C merens \ -o OUTPUT.fa \ --hmm-source Campbell_et_al \ --gene-names Ribosomal_L27,Ribosomal_L28,Ribosomal_L3 \ --return-best-hit \ --get-aa-sequences \ --concatenate

Edit this file to update this information.

Additional Resources

Are you aware of resources that may help users better understand the utility of this program? Please feel free to edit this file on GitHub. If you are not sure how to do that, find the __resources__ tag in this file to see an example.