ISeqDb 0.0.3

ISeqDb - Identify Sequences in Databases

##ISeqDb - Identify Sequences in Databases

Screening of query dna sequences for the presence of specific target genes or proteins.

Query sequences can be metagenome assembles genomes (MAGs), contigs/scaffolds, multifasta and fasta files. Typically, databases contain multifasta homologous sequences. Databases are queried using megablast, blastn and blastx.

ISeqDd was tested to search for target genes or proteins in bacterial MAGs. ISeqDb was written primarily to search for the presence of genes encoding cyanotoxins and other genes encoding metabolites hazardous to human health in cyanobacterial MAGs. Currently available databases include DNA sequences of genes encoding microcystins (mcyB, mcyD, mcyE), anatoxins (anaC, anaF) and geosmin (geoA).

Any other database of homologous sequences can be used. This includes, for example, the rbcL gene used to classify diatoms (included). Additional nucleotide or protein databases may be created using the create_db module.

Installation

Requirements

python>=3.10, pandas, blast>=2.15, pip

conda/mamba should be already installed (https://mamba.readthedocs.io/en/latest/)

conda and pip

• Install dependencies creating a conda environment (through conda or mamba)

mamba create --name ISeqDb python>=3.10

mamba activate ISeqDb

mamba install -c bioconda -c conda-forge python>=3.10 pandas blast>=2.15 pip

• Install ISeqDb

pip install ISeqDb

Basic usage

ISeqDb has three modules:

find_nucl: Identify sequences in databases using megablast, blastn or blastx ISeqDb find_nucl /path_to/queryfile.fasta /path_to/targetdatabase.tar.gz /path_to/outputfile.txt

inspect_db: Inspect or save the sequence database ISeqDb inspect_db /path_to/arch.tar.gz -- (inspect database) ISeqDb inspect_db /path_to/arch.tar.gz -d /outdir -- (inspect and save a copy arch.fasta)

create_db: Create a database from a fasta/multifasta file using makeblast ISeqDb create_db /path_to/arch.fasta -m "nucl" -- (nucleotide archives) ISeqDb create_db /path_to/arch.fasta -m "prot" -- (protein archives)

Usage

#####find_nucl

######positional arguments:

queryfile Input query file fasta/multi-fasta (with path) - e.g. /dir/query.fna

targetdb Target database for the blast analysis (with path) - e.g. /dir/arch.tar.gz

outputfile Output name file (with path) - e.g. /dir/out.txt

######options:

-h, --help show this help message and exit

-k {megablast,blastn,blastx}, --task {megablast,blastn,blastx} Task: megablast (nucl), blastn (nucl), blastx (prot); default=megablast

-m MAXTARGSEQ, --maxtargseq MAXTARGSEQ -Keep max target sequences >= maxtargseq; default=100

-e MINEVALUE, --minevalue MINEVALUE Keep hits with evalue >= minevalue; default=1e-6

-p MINPIDENT, --minpident MINPIDENT Keep hits with pident >= minpident (only megablast/blastn); default=85

-t THREADS, --threads THREADS Number of threads to use; default=1

-s SORTOUTPUT, --sortoutput SORTOUTPUT Sort output by colname. eg.: bitscore, pident, alignment_length; default=bitscore

-d {comma,semicolon,tab}, --delimiter {comma,semicolon,tab} Output delimiter: comma, semicolon, tab; default=comma

######Output legend (in square brackets, the blast codes)

query_id: query/sequence identifier [qacc] subject_accession: NCBI accession number or subject identifier in the database [sacc] pident: percentage of identical matches in query and subject sequences [pident] n_ident_match: number of identical bases/matches [nident] n_diff_match: number of different bases/matches [mismatch] n_gaps: total number of gaps [gaps] alignment_length: length of the alignemnt between query and subject sequences [length] query_start_al: start of alignment in query [qstart] query_end_al: end of alignment in query [qend] subj_start_al: start of alignment in subject [sstart] subj_end_al: end of alignment in subject [send] bitscore: bit score [bitscore] evalue: expect value [evalue] subject_seq_title: title of subject sequence in database [stitle] align_query_seq: aligned part of query sequence [qseq] align_subj_seq: aligned part of subject sequence [sseq]

######example: ISeqDb find_nucl
/inputdir/file_nucleotite.fna
/archdir/mcyE.tar.gz
/outdir/ISeqDb_output.txt
-k "megablast" -p 95 -e 1e-16 -t 8 -d "tab" -s "pident"

#####inspect_db

######positional arguments: targetdb Target database (with path) - e.g. /dir/arch.tar.gz

######options: -h, --help show this help message and exit

-d SAVEDB, --savedb SAVEDB Output directory (with path) - e.g. /dir/; if not indicated, default=nosave

######example: ISeqDb inspect_db
/archdir/mcyB.tar.gz
-d /outdir/

#####create_db

######positional arguments: targetfasta Fasta file (with path) - e.g. /dir/arch.fasta

######options: -h, --help show this help message and exit

-m {nucl,prot}, --moltype {nucl,prot} Molecule type in fasta file, nucl (nucleotide) or prot (protein)

######example: ISeqDb create_db
/inputdir/geneseq.fna
-m "nucl"

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#####ISeqDb relies on BLAST®:

• BLAST® Command Line Applications User Manual [Internet]. Bethesda (MD): National Center for Biotechnology Information (US); 2008-.
• Camacho C., Coulouris G., Avagyan V., Ma N., Papadopoulos J., Bealer K., Madden T.L. (2008) “BLAST+: architecture and applications.” BMC Bioinformatics 10:421. PubMed