Submit query
     
Click here to show/hide the option menu Clear this form Show help for the chosen program
  • Select the program of choice.
  • Paste your query in the query box. Click Submit button to pass on the query with default options. Please note that some programs might have some options/parameters that are required. Also note that SeWeR doesn't check whether the required option(s)/parameter(s) is supplied or not. See program description for details.
  • Click Options button to fill up options. The button is a toggle. Clicking it again will close the option.
  • Click Customize to customize this search. Fill up all the options that you require, then click Customize. SeWeR will open another window with a customized page. Save that file on your computer.
  • Click Help to check the help page of the selected program. SeWeR will open a new window to show the help page.
  • Click Submit to pass on the query. SeWeR will open a new window for results.
Home | NucleicAcid | Protein | Database | PCR | Alignment | Tools | Bookmarklets | Customize

Copyright © 2000 Malay Kumar Basu
Send your comments/suggestions/bug-report to me:
curiouser@ccmb.ap.nic.in
Disclaimer
readseq
Output format
cap
Remove bad 5' and 3' regions of each fragment
Yes No		 Trim the sequencing/cloning vector from each fragment
Yes No
Assembly algorithm
Cap 3
Cap2 - optimized for reads <= 450 bp
Cap2 - optimized for reads > 450 bp
 Results
Interactively
By email Address
ReadSeq
At Baylor College of medicine. ReadSeq is written by Don Gilbert. It automatically recognizes the input sequence type and convert it into a format of choice. Input type-DNA/protein sequence(s)of different formats. Required option-output format.
CAP
Contig assembly program (CAP). Input type-DNA sequences in FASTA format. Required option-none.

TOOLS
Clean/Inverse Complement
BIOSED
Replace or delete sequence sections (EMBOSS). Input type: sequence [sequences] (-sequence).
Required options: email sequence target outseq.

biosed

Your email:

Sequence section to match (-target)

Delete the target sequence sections (-delete)

Replacement sequence section (-replace)

outseq (-outseq)

Output format for: outseq

CUTSEQ
Removes a specified section from a sequence. (EMBOSS). Input type: sequence -- gapany [single sequence] (-sequence).
Required options: email sequence from to outseq.

cutseq

Your email:

Start of region to delete (-from)

End of region to delete (-to)

outseq (-outseq)

Output format for: outseq

DEGAPSEQ
Removes gap characters from sequences (EMBOSS). Input type: sequence -- gapany [sequences] (-sequence).
Required options: email sequence outseq.

degapseq

Your email:

outseq (-outseq)

Output format for: outseq

DESCSEQ
Alter the name or description of a sequence. (EMBOSS). Input type: sequence -- gapany [single sequence] (-sequence).
Required options: email sequence outseq.

descseq

Your email:

Name of the sequence (-name)

Description of the sequence (-description)

Append to the existing description (-append)

outseq (-outseq)

Output format for: outseq

EXTRACTSEQ
Extract regions from a sequence (EMBOSS). Input type: sequence -- any [sequences] (-sequence).
Required options: email sequence regions outseq.

extractseq

Your email:

Regions to extract (eg: 4-57,78-94) (-regions)

Write regions to separate sequences (-separate)

outseq (-outseq)

Output format for: outseq

LISTOR
Writes a list file of the logical OR of two sets of sequences (EMBOSS). Input type: firstset [set of sequences] (-firstset).
Required options: email firstset secondset operator outlist.

listor

Your email:


secondset [set of sequences] (-secondset)

Enter the logical operator to combine the sequences -- Logical operator to combine sequence lists (-operator)

Output list file (-outlist)

MASKSEQ
Mask off regions of a sequence. (EMBOSS). Input type: sequence -- any [single sequence] (-sequence).
Required options: email sequence regions outseq.

maskseq

Your email:

Regions to mask (eg: 4-57,78-94) (-regions)

outseq (-outseq)

Output format for: outseq

Character to mask with (-maskchar)

NEWSEQ
Type in a short new sequence. (EMBOSS). Input type: .
Required options: email outseq name description type sequence.

newseq

Your email:

outseq (-outseq)

Output format for: outseq

Name of the sequence (-name)

Description of the sequence (-description)

Type of sequence -- Type of sequence (-type)

Enter the sequence (-sequence)

NOTSEQ
Excludes a set of sequences and writes out the remaining ones (EMBOSS). Input type: sequence [sequences] (-sequence).
Required options: email sequence exclude outseq.

notseq

Your email:

Sequence names to exclude (-exclude)

outseq (-outseq)

Output format for: outseq

file of excluded sequences (-junkout)

Output format for: file of excluded sequences

NTHSEQ
Writes one sequence from a multiple set of sequences (EMBOSS). Input type: sequence [sequences] (-sequence).
Required options: email sequence number outseq.

nthseq

Your email:

The number of the sequence to output (-number)

outseq (-outseq)

Output format for: outseq

PASTESEQ
Insert one sequence into another (EMBOSS). Input type: sequence -- any [single sequence] (-sequence).
Required options: email sequence insseq pos outseq.

pasteseq

Your email:


Sequence to insert (-insseq)

Position to insert after (-pos)

outseq (-outseq)

Output format for: outseq

REVSEQ
Reverse and complement a sequence (EMBOSS). Input type: sequence -- dna [sequences] (-sequence).
Required options: email sequence outseq.

revseq

Your email:

Reverse sequence (-reverse)

Complement sequence (-complement)

outseq (-outseq)

Output format for: outseq

SPLITTER
Split a sequence into (overlapping) smaller sequences (EMBOSS). Input type: sequence -- any [sequences] (-sequence).
Required options: email sequence outseq.

splitter

Your email:

Size to split at (-size)

Overlap between split sequences (-overlap)

outseq (-outseq)

Output format for: outseq

TRIMEST
Trim poly-A tails off EST sequences (EMBOSS). Input type: sequence -- dna [sequences] (-sequence).
Required options: email sequence outseq.

trimest

Your email:

Minimum length of a poly-A tail (-minlength)

Number of contiguous mismatches allowed in a tail (-mismatches)

Write the reverse complement when poly-T is removed (-reverse)

Remove poly-T tails at the 5' end of the sequence. (-fiveprime)

outseq (-outseq)

Output format for: outseq

TRIMSEQ
Trim ambiguous bits off the ends of sequences (EMBOSS). Input type: sequence -- gapany [sequences] (-sequence).
Required options: email sequence outseq.

trimseq

Your email:

Window size (-window)

Percent threshold of ambiguity in window (-percent)

Trim off all ambiguity codes, not just N or X (-strict)

Trim off asterisks (-star)

Trim at the start (-left)

Trim at the end (-right)

outseq (-outseq)

Output format for: outseq

VECTORSTRIP
Strips out DNA between a pair of vector sequences (EMBOSS). Input type: sequence -- dna [sequences] (-sequence).
Required options: email sequence vectors outf outseq.

vectorstrip

Your email:

Are your vector sequences in a file? (-vectorfile)


Name of vectorfile (-vectors)

Max allowed % mismatch (-mismatch)

Show only the best hits (minimise mismatches)? (-besthits)

5' sequence (-linkera)

3' sequence (-linkerb)

outf (-outf)

outseq (-outseq)

Output format for: outseq