Submit your metagenome data to OPAR Optimistic Protein assembly from reads
It will try to assemble potentially novel proteins from your reads

1Contact Information: give us a way to notify you when the job is done

Your Full Name Email Address Job name

2Data to submit: choose the type of job and provide the files for it

Uploaded files are assumed to be fasta or fastq format. Compressed files (.gz) are accepted

Please remove spaces from the tags or headers. OPAR automatically replaces spaces in headers with underscores (_); however, the tags no longer match the original submitted set of reads. To create a FASTA input file without spaces in headers use this PYTHON script script to remove spaces from FASTA file

Choose the type of job^{see footnotes} Reads (fasta/fastq/gz) Target Protein (fasta/tab)

3Parameters for alignments: change the sensitivity of the search

e-value alignments per read (Between 1 and 25) maximum number of "contigs" to attempt (Between 0 and 100)

^Footnotes:

The job options are targeted to the following purposes

reads against proteins database(DIAMOND/nr): provided set of reads is compared against all known proteins
reads against viral proteins database(DIAMOND/nr_vir): provided set of reads is compared against all known viral proteins
(option removed due to execution time) reads against nucleotide database(blastn/nt): provided set of reads is compared against all known nucleotide sequences
reads against viral nucleotide database(blastn/nt_vir): provided set of reads is compared against all known viral nucleotide sequences
reads against provided protein(blastx/provided fasta): provided set of reads is compared to a specific protein provided by the user
reads against provided nucleotide sequence(blastn/provided fasta): provided set of reads is compared to a specific sequence provided by the user
only assembly from provided BLAST-tabbed file and reads(only assembly): provided set of reads is assembled according to the alignments in the BLAST-tabbed provided by the user, i.e. the assembly is attempted without the alignment phase

This project takes advantage of tools developed by other research teams; if you use this website for your own research, please make sure to include the corresponding references:

DIAMOND is used to align reads to protein databases. Please visit the site to know more: Diamond
blastn is used to align reads to nucleotide databases or provided nucleotide sequence. Please visit the online version of the tool to know more: Blastn
blastx is used to align reads to provided protein sequence. Please visit the online version of the tool to know more: Blastx
OPAR is developed to put together multiple tools and simplify the salvage of sequences in sets of reads. If you use this tool project, please cite An optimistic protein assembly from sequence reads salvaged an uncharacterized segment of mouse picobirnavirus

The PERL script used to create the commands to these tools and assemble the "contigs" out of the alignment information is available for downloading here

A simplified PERL script only for the assembly phase (like the last option) is available for downloading here

Submit your metagenome data to OPAR Optimistic Protein assembly from readsIt will try to assemble potentially novel proteins from your reads

Submit your metagenome data to OPAR Optimistic Protein assembly from reads
It will try to assemble potentially novel proteins from your reads