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Input form  |  Web services  |  Help & Documentation  |  Bioinformatics Tools FAQ

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.

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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 in GCG, FASTA, EMBL (Nucleotide only), GenBank, PIR, NBRF, PHYLIP or UniProtKB/Swiss-Prot (Protein only) format. Partially formatted sequences are not accepted. (See example input formats). 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. There is a limit of 2MB.

Sequence File Upload

A file containing one or more valid sequences in any format (GCG, FASTA, EMBL (Nucleotide only), GenBank, PIR, NBRF, PHYLIP or UniProtKB/Swiss-Prot (Protein only)) can be uploaded and used as input for the translation. (See example input formats). 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. There is a limit of 2MB.

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.

TypeAbbreviation
PROTEINprotein
DNAdna
RNArna

Step 2 - Select parameters

Input Format

Input format name

Format NameValue
Unknown formatunknown
GCG sequence formatgcg
GCG old (version 8) sequence formatgcg8
EMBL entry formatembl
Swissprot entry formatswiss
NBRF/PIR entry formatnbrf
PDB protein databank format ATOM linespdb
PDB protein databank format SEQRES linespdbseq
PDB protein databank format nucleotide ATOM linespdbnuc
PDB protein databank format nucleotide SEQRES linespdbnucseq
FASTA format including NCBI-style IDsfasta
Plain old fasta format with IDs not parsed furtherpearson
FASTQ short read format ignoring quality scoresfastq
FASTQ short read format with phred qualityfastq-sanger
FASTQ Illumina 1.3 short read formatfastq-illumina
FASTQ Solexa/Illumina 1.0 short read formatfastq-solexa
Sequence Alignment/Map (SAM) formatsam
Genbank entry formatgenbank
Genbank/DDBJ entry format (alias)ddbj
Refseq entry formatrefseq
Refseq protein entry formatrefseqp
Codata entry formatcodata
DNA strider output formatstrider
Clustalw output formatclustal
Phylip interleaved and non-interleaved formatsphylip
Phylip non-interleaved formatphylipnon
ACE sequence formatace
ACE sequence formatconsed
ACEDB sequence formatacedb
Fasta format variant with database name before IDdbid
GCG MSF (multiple sequence file) file formatmsf
Hennig86 output formathennig86
Jackknifer interleaved and non-interleaved formatsjackknifer
Nexus/paup interleaved formatnexus
Treecon output formattreecon
Mega interleaved and non-interleaved formatsmega
Intelligenetics sequence format strict parserigstrict
Intelligenetics sequence formatig
Old staden package sequence formatstaden
Plain texttext
GFF feature file with sequence in the headergff2
GFF3 feature file with sequencegff3
GFF3 feature file with sequencegff
Stockholm (pfam) formatstockholm
Selex formatselex
Fitch program formatfitch
Biomart tab-delimited resultsbiomart
Mase program formatmase
Raw sequence with no non-sequence charactersraw
Staden experiment fileexperiment
ABI trace fileabi
Binary Sequence Alignment/Map (BAM) formatbam
Ensembl SQL formatensembl

Default value is: Unknown format [unknown]

Output Format

Output format name. Example output formats

Format NameValue
EMBL entry formatembl
Unknown formatunknown
GCG sequence formatgcg
GCG old (version 8) sequence formatgcg8
EMBL new entry formatemblnew
Swissprot entry formatswiss
Swissprot entry format (swold)swold
Swissprot entry format (swissold)swissold
Swissprot entry format (swissprotold)swissprotold
Swissprot entry format (swissnew)swissnew
FASTA formatfasta
NCBI fasta format with NCBI-style IDsncbi
NCBI fasta format with NCBI-style IDs using GI numbergifasta
NBRF/PIR entry formatnbrf
Genbank entry formatgenbank
Genbank/DDBJ entry format (alias)ddbj
Genpept entry formatgenpept
Refseq entry formatrefseq
Refseqp entry formatrefseqp
GFF2 feature file with sequence in the headergff2
GFF3 feature file with sequence in FASTA format aftergff3
GFF3 feature file with sequence in FASTA format aftergff
Intelligenetics sequence formatig
Codata entry formatcodata
DNA strider output formatstrider
ACEDB sequence formatacedb
Staden experiment fileexperiment
Old staden package sequence formatstaden
Plain texttext
Fitch program formatfitch
GCG MSF (multiple sequence file) file formatmsf
Clustalw multiple alignment formatclustal
Selex formatselex
Phylip interleaved formatphylip
Phylip non-interleaved formatphylipnon
NCBI ASN.1 formatasn1
Hennig86 output formathennig86
Mega interleaved output formatmega
Mega non-interleaved output formatmeganon
Nexus/paup interleaved formatnexus
Nexus/paup non-interleaved formatnexusnon
Jackknifer output interleaved formatjackknifer
Jackknifer output non-interleaved formatjackknifernon
Treecon output formattreecon
Mase program formatmase
DASDNA DAS nucleotide-only sequencedasdna
DASSEQUENCE DAS any sequencedas
FASTQ short read format with phred qualityfastq-sanger
FASTQ short read format with phred qualityfastq
FASTQ Illumina 1.3 short read formatfastq-illumina
FASTQ Solexa/Illumina 1.0 short read formatfastq-solexa
Sequence alignment/map (SAM) formatsam
Binary sequence alignment/map (BAM) formatbam
Debugging trace of full internal data contentdebug

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).

References

EMBOSS: the European Molecular Biology Open Software Suite.
(2000 June 01) Trends in genetics : TIG 16 (6) :276-277
PMID: 10827456The EMBL-EBI bioinformatics web and programmatic tools framework.
(2015 April 06) Nucleic acids research 43 (W1) :W580-4
PMID: 25845596Analysis Tool Web Services from the EMBL-EBI.
(2013 May 13) Nucleic acids research 41 (Web Server issue) :W597-600
PMID: 23671338


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