Readseq

Introduction

Readseq reads and converts biosequences between a selection of common biological sequence formats, including EMBL, GenBank and fasta sequence formats.

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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 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. There is a 2MB limit.

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. There is a 2MB limit.

Step 2 - Select parameters

Input Format

Input format name

Format Name Value
Auto-detected 0
EMBL 4
GenBank 2
Fasta(Pearson) 8
Clustal/ALN 22
ACEDB 25
BLAST 20
DNAStrider 6
FlatFeat/FFF 23
GCG 5
GFF 24
IG/Stanford 1
MSF 15
NBRF 3
PAUP/NEXUS 17
Phylip(Phylip4) 12
Phylip3.2 11
PIR/CODATA 14
Plain/Raw 13
SCF 21
XML 19

Default value is: Auto-detected [0]

Output Format

Output format name.

Format Name Value
EMBL 4
GenBank 2
Fasta(Pearson) 8
Clustal/ALN 22
ACEDB 25
DNAStrider 6
FlatFeat/FFF 23
GCG 5
GFF 24
IG/Stanford 1
MSF 15
NBRF 3
PAUP/NEXUS 17
Phylip(Phylip4) 12
Phylip3.2 11
PIR/CODATA 14
Plain/Raw 13
Pretty 18
XML 19

Default value is: EMBL [4]

Output Case

Change alphabet case for output sequences.

Default value is: No change [none]

Remove Gap Symbols

Remove gap symbols for output sequences.

label value
None none
Symbol - -
Symbol . .

Default value is: None [none]

Reverse-Complement of Input Sequencess

Reverse-complement of input sequences

Default value is: no [false]

Translate Symbols

Translate input symbol to output symbol.

Default value is:

Feature Selection

Feature to select

Feature Description
attenuator
C_region
CAAT_signal
CDS
conflict
D-loop
D_segment
enhancer
exon
GC_signal
gene
iDNA
intron
J_segment
LTR
mat_peptide
misc_binding
misc_difference
misc_feature
misc_recomb
misc_RNA
misc_signal
misc_structure
modified_base
mRNA
N_region
old_sequence
polyA_signal
polyA_site
precursor_RNA
prim_transcript
primer_bind
promoter
protein_bind
RBS
repeat_region
repeat_unit
rep_origin
rRNA
S_region
satellite
scRNA
sig_peptide
snRNA
source
stem_loop
STS
TATA_signal
terminator
transit_peptide
tRNA
unsure
V_region
V_segment
variation
3'clip
3'UTR
5'clip
5'UTR
-10_signal
-35_signal
-

Feature Handle

Handling selectd features - to remove or extract sequence of selected features.

label value
None none
Remove sequence of selected features remove
Extract sequence of selected features extract

Default value is: None [none]

Subrange

Subrange of sequence feature locations to extract. E.g., -1000..0 -- 1000 bases upstream to start of feature; 1..end1 -- the full range of the feature; end1..end100 -- from the end to 100 bases downstream of the feature; -100..end100 -- 100 bases upstream to 100 bases downstream; join-100..10,end1..end100 -- 100 bases upstream to 10 into joined with the end to 100 bases downstream.

Default value is:

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

Sequence file format conversion with command-line readseq.
(2003 Feb) Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.] Appendix 1 :Appendix 1E
A new bioinformatics analysis tools framework at EMBL-EBI.
(2010 Jul) Nucleic acids research 38 (Web Server issue) :W695-9
Analysis Tool Web Services from the EMBL-EBI.
(2013 Jul) Nucleic acids research 41 (Web Server issue) :W597-600