EMBOSS Seqret
Introduction
EMBOSS Seqret reads and writes (returns) sequences. It is useful for a variety of tasks, including extracting sequences from databases, displaying sequences, reformatting sequences, producing the reverse complement of a sequence, extracting fragments of a sequence, sequence case conversion or any combination of the above functions.
- Download Software
How to use this tool
Running a tool from the web form is a simple multiple steps process, starting at the top of the page and following the steps to the bottom.
Each tool has at least 2 steps, but most of them have more:
- The first steps are usually where the user sets the tool input (e.g. sequences, databases...)
- In the following steps, the user has the possibility to change the default tool parameters
- And finally, the last step is always the tool submission step, where the user can specify a title to be associated with the results and an email address for email notification. Using the submit button will effectively submit the information specified previously in the form to launch the tool on the server
Note that the parameters are validated prior to launching the tool on the server and in the event of a missing or wrong combination of parameters, the user will be notified directly in the form.
Step 1 - Input Sequences
Input Sequence
One or more sequences to be translated can be entered directly into this form. Sequences can be be in GCG, FASTA, EMBL, GenBank, PIR, NBRF, PHYLIP or UniProtKB/Swiss-Prot format. Partially formatted sequences are not accepted. Adding a return to the end of the sequence may help certain applications understand the input. Note that directly using data from word processors may yield unpredictable results as hidden/control characters may be present.
Sequence File Upload
A file containing one or more valid sequences in any format (GCG, FASTA, EMBL, GenBank, PIR, NBRF, PHYLIP or UniProtKB/Swiss-Prot) can be uploaded and used as input for the translation. Word processor files may yield unpredictable results as hidden/control characters may be present in the files. It is best to save files with the Unix format option to avoid hidden Windows characters.
Sequence Type
Indicates if the query sequence is protein, DNA or RNA. Used to force FASTA to interpret the input sequence as specified type of sequence (via. the '-p', '-n' or '-U' options), this prevents issues when using nucleotide sequences that contain many ambiguous residues.
| Type | Abbreviation |
|---|---|
| PROTEIN | protein |
| DNA | dna |
| RNA | rna |
Step 2 - Select parameters
Input Format
Input format name
| Format Name | Value |
|---|---|
| Unknown format | unknown |
| GCG sequence format | gcg |
| GCG old (version 8) sequence format | gcg8 |
| EMBL entry format | embl |
| Swissprot entry format | swiss |
| NBRF/PIR entry format | nbrf |
| PDB protein databank format ATOM lines | pdb |
| PDB protein databank format SEQRES lines | pdbseq |
| PDB protein databank format nucleotide ATOM lines | pdbnuc |
| PDB protein databank format nucleotide SEQRES lines | pdbnucseq |
| FASTA format including NCBI-style IDs | fasta |
| Plain old fasta format with IDs not parsed further | pearson |
| FASTQ short read format ignoring quality scores | fastq |
| FASTQ short read format with phred quality | fastq-sanger |
| FASTQ Illumina 1.3 short read format | fastq-illumina |
| FASTQ Solexa/Illumina 1.0 short read format | fastq-solexa |
| Sequence Alignment/Map (SAM) format | sam |
| Genbank entry format | genbank |
| Genbank/DDBJ entry format (alias) | ddbj |
| Refseq entry format | refseq |
| Refseq protein entry format | refseqp |
| Codata entry format | codata |
| DNA strider output format | strider |
| Clustalw output format | clustal |
| Phylip interleaved and non-interleaved formats | phylip |
| Phylip non-interleaved format | phylipnon |
| ACE sequence format | ace |
| ACE sequence format | consed |
| ACEDB sequence format | acedb |
| Fasta format variant with database name before ID | dbid |
| GCG MSF (multiple sequence file) file format | msf |
| Hennig86 output format | hennig86 |
| Jackknifer interleaved and non-interleaved formats | jackknifer |
| Nexus/paup interleaved format | nexus |
| Treecon output format | treecon |
| Mega interleaved and non-interleaved formats | mega |
| Intelligenetics sequence format strict parser | igstrict |
| Intelligenetics sequence format | ig |
| Old staden package sequence format | staden |
| Plain text | text |
| GFF feature file with sequence in the header | gff2 |
| GFF3 feature file with sequence | gff3 |
| GFF3 feature file with sequence | gff |
| Stockholm (pfam) format | stockholm |
| Selex format | selex |
| Fitch program format | fitch |
| Biomart tab-delimited results | biomart |
| Mase program format | mase |
| Raw sequence with no non-sequence characters | raw |
| Staden experiment file | experiment |
| ABI trace file | abi |
| Binary Sequence Alignment/Map (BAM) format | bam |
| Ensembl SQL format | ensembl |
Default value is: Unknown format [unknown]
Output Format
Output format name.
| Format Name | Value |
|---|---|
| EMBL entry format | embl |
| Unknown format | unknown |
| GCG sequence format | gcg |
| GCG old (version 8) sequence format | gcg8 |
| EMBL new entry format | emblnew |
| Swissprot entry format | swiss |
| Swissprot entry format (swold) | swold |
| Swissprot entry format (swissold) | swissold |
| Swissprot entry format (swissprotold) | swissprotold |
| Swissprot entry format (swissnew) | swissnew |
| FASTA format | fasta |
| NCBI fasta format with NCBI-style IDs | ncbi |
| NCBI fasta format with NCBI-style IDs using GI number | gifasta |
| NBRF/PIR entry format | nbrf |
| Genbank entry format | genbank |
| Genbank/DDBJ entry format (alias) | ddbj |
| Genpept entry format | genpept |
| Refseq entry format | refseq |
| Refseqp entry format | refseqp |
| GFF2 feature file with sequence in the header | gff2 |
| GFF3 feature file with sequence in FASTA format after | gff3 |
| GFF3 feature file with sequence in FASTA format after | gff |
| Intelligenetics sequence format | ig |
| Codata entry format | codata |
| DNA strider output format | strider |
| ACEDB sequence format | acedb |
| Staden experiment file | experiment |
| Old staden package sequence format | staden |
| Plain text | text |
| Fitch program format | fitch |
| GCG MSF (multiple sequence file) file format | msf |
| Clustalw multiple alignment format | clustal |
| Selex format | selex |
| Phylip interleaved format | phylip |
| Phylip non-interleaved format | phylipnon |
| NCBI ASN.1 format | asn1 |
| Hennig86 output format | hennig86 |
| Mega interleaved output format | mega |
| Mega non-interleaved output format | meganon |
| Nexus/paup interleaved format | nexus |
| Nexus/paup non-interleaved format | nexusnon |
| Jackknifer output interleaved format | jackknifer |
| Jackknifer output non-interleaved format | jackknifernon |
| Treecon output format | treecon |
| Mase program format | mase |
| DASDNA DAS nucleotide-only sequence | dasdna |
| DASSEQUENCE DAS any sequence | das |
| FASTQ short read format with phred quality | fastq-sanger |
| FASTQ short read format with phred quality | fastq |
| FASTQ Illumina 1.3 short read format | fastq-illumina |
| FASTQ Solexa/Illumina 1.0 short read format | fastq-solexa |
| Sequence alignment/map (SAM) format | sam |
| Binary sequence alignment/map (BAM) format | bam |
| Debugging trace of full internal data content | debug |
Default value is: EMBL entry format [embl]
Feature Selection
Use feature information
Default value is: yes [true]
First Sequence Only
Read one sequence and stop
Default value is: no [false]
Reverse-Complement of Input Sequencess
Reverse-complement of input DNA sequences
Default value is: no [false]
Output Case
Change alphabet case for output sequences.
Default value is: No change [none]
Sequence Range
Specify a range or section of the input sequence to use in the search. Example: Specifying '34-89' in an input sequence of total length 100, will tell EMBOSS seqret to only use residues 34 to 89, inclusive.
Default value is: START-END
Step 3 - Submission
Job title
It's possible to identify the tool result by giving it a name. This name will be associated to the results and might appear in some of the graphical representations of the results.
Email Notification
Running a tool is usually an interactive process, the results are delivered directly to the browser when they become available. Depending on the tool and its input parameters, this may take quite a long time. It's possible to be notified by email when the job is finished by simply ticking the box "Be notified by email". An email with a link to the results will be sent to the email address specified in the corresponding text box. Email notifications require valid email addresses.
Email Address
If email notification is requested, then a valid Internet email address in the form joe@example.org must be provided. This is not required when running the tool interactively (The results will be delivered to the browser window when they are ready).