Cross-species protein sequence and gene structure prediction with fine-tuned Webscipio 2.0 and Scipio.

Leave a Comment / Cross-species protein sequence and gene structure prediction with fine-tuned Webscipio 2.0 and Scipio. / By

BACKGROUNDObtaining transcript homologs closely related organisms and take reconstructed exon-intron gene pattern is a very important process for the analysis of protein family evolution and comparative analysis of the exon-intron structure of particular genes of various types. Due to ever-increasing speed of genome sequencing, genome explanation gap to develop.

Thus, the correct tools for the prediction and reconstruction of genes in related organisms become more and more important. Scipio tool, which can also be used through a graphical interface WebScipio, perform processing significant hit from the output of the program Blat into account sequencing errors, missing sequence and genome assemblies fragmented. However, Scipio so far been restricted to high sequence similarity and can reconstruct short exons.

RESULTSScipio and WebScipio has fundamentally been extended to better reconstruct the very short exons and intron splice sites and would be better suited for cross-species gene structure prediction. Needleman-Wunsch algorithm has been implemented to look for short portions of the query sequence that is not recognized by the Blat.

The regions may be short exons, a different sequence in the intron splice sites, or exon very different. We have demonstrated the benefit and use of the new parameters with a few examples of the protein family of proteins that are completely different in the search for the species from several kingdoms of eukaryotes. Performance Scipio new version has been tested in comparison with some kind tools.

CONCLUSIONSWith new version of Scipio exon very short, terminal and internal, even just one amino acid can be completely reconstructed. Scipio was also able to correctly predict almost all cross-species gene searches even if the ancestors of separate species more than 100 Myr ago and if the identity of the protein sequences under 80%. For our test case Scipio surpasses all other software we tested.

A4GNT Peptide
MBS3233441-5x01mg 5x0.1mg
EUR 730

A4GNT Antibody
8C14412 50ug
EUR 368
Description: A4GNT Antibody

A4GNT antibody
70R-7408 50 ug
EUR 467
Description: Rabbit polyclonal A4GNT antibody raised against the N terminal of A4GNT

A4GNT antibody
70R-7409 50 ug
EUR 467
Description: Rabbit polyclonal A4GNT antibody raised against the C terminal of A4GNT

A4GNT Antibody
34406 100ul
EUR 319

A4GNT Antibody
34406-100ul 100ul
EUR 302.4

A4GNT Antibody
34406-50ul 50ul
EUR 224.4

A4GNT antibody
70R-34020 100 ug
EUR 294
Description: Rabbit polyclonal A4GNT antibody

A4GNT antibody
70R-36130 100 ug
EUR 420
Description: Rabbit polyclonal A4GNT antibody

A4GNT antibody
70R-50979 100 ul
EUR 242
Description: Purified Polyclonal A4GNT antibody

A4GNT Antibody
ABD3762 100 ug
EUR 525.6

A4GNT Antibody
1-CSB-PA072731
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  • 50ul
  • 100ul
Description: A polyclonal antibody against A4GNT. Recognizes A4GNT from Human. This antibody is Unconjugated. Tested in the following application: ELISA, IHC;ELISA:1:2000-1:5000, IHC:1:25-1:100

A4GNT Antibody
1-CSB-PA001009LA01HU
  • Ask for price
  • Ask for price
  • 50ug
  • 100ug
Description: A polyclonal antibody against A4GNT. Recognizes A4GNT from Human. This antibody is Unconjugated. Tested in the following application: ELISA, IHC; Recommended dilution: IHC:1:20-1:200

A4GNT Antibody
CSB-PA797885- each
EUR 402
Description: A polyclonal antibody against A4GNT. Recognizes A4GNT from Human. This antibody is Unconjugated. Tested in the following application: ELISA, WB;WB:1:500-1:3000

A4GNT Antibody
CSB-PA797885-100ul 100ul
EUR 379.2
Description: A polyclonal antibody against A4GNT. Recognizes A4GNT from Human. This antibody is Unconjugated. Tested in the following application: ELISA, WB;WB:1:500-1:3000

A4GNT Antibody
1-CSB-PA020263
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  • 50ug
  • 100ug
Description: A polyclonal antibody against A4GNT. Recognizes A4GNT from Human. This antibody is Unconjugated. Tested in the following application: WB, IHC, ELISA;WB:1/500-1/2000.IHC:1/100-1/300.ELISA:1/40000

A4GNT Antibody
1-CSB-PA703896
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  • 50ul
  • 100ul
Description: A polyclonal antibody against A4GNT. Recognizes A4GNT from Human. This antibody is Unconjugated. Tested in the following application: ELISA, IHC;ELISA:1:2000-1:5000, IHC:1:25-1:100

A4GNT Antibody
E034406 100μg/100μl
EUR 255
Description: Available in various conjugation types.

A4GNT Antibody
DF3762 200ul
EUR 420

A4GNT Antibody
DF3762-100ul 100ul
EUR 168
Description: WB,IF/ICC,ELISA(peptide)

A4GNT Antibody
DF3762-200ul 200ul
EUR 210
Description: WB,IF/ICC,ELISA(peptide)

A4GNT Antibody
CAC11724-100ug 100ug
EUR 314

A4GNT Antibody
CAC11724-50ug 50ug
EUR 199.2

A4GNT Antibody
E11-14412C 100μg
EUR 225
Description: Available in various conjugation types.

A4GNT Antibody
E306208 100ug/200ul
EUR 275
Description: Available in various conjugation types.

A4GNT Antibody
E38PA2660 100ul
EUR 225
Description: Available in various conjugation types.

A4GNT Antibody
E19-3762 100μg/100μl
EUR 225
Description: Available in various conjugation types.

A4GNT Antibody
GWB-MQ692H 50ug Ask for price

A4GNT Antibody
GWB-MQ693I 50ug Ask for price

A4GNT Antibody
MBS5315597-01mL 0.1mL
EUR 470

A4GNT Antibody
MBS5315597-5x01mL 5x0.1mL
EUR 1955

A4GNT Antibody
MBS5313371-01mg 0.1mg
EUR 635

A4GNT Antibody
MBS5313371-5x01mg 5x0.1mg
EUR 2705

A4GNT Antibody
MBS7003297-005mg 0.05mg
EUR 190

A4GNT Antibody
MBS7003297-01mg 0.1mg
EUR 270

A4GNT Antibody
MBS7003297-5x01mg 5x0.1mg
EUR 1205

A4GNT Antibody
MBS7124483-005mL 0.05mL
EUR 190

A4GNT Antibody
MBS7124483-01mL 0.1mL
EUR 270

A4GNT Antibody
MBS7124483-5x01mL 5x0.1mL
EUR 1205

A4GNT Antibody
MBS7124484-005mL 0.05mL
EUR 190

A4GNT Antibody
MBS7124484-01mL 0.1mL
EUR 270

A4GNT Antibody
MBS7124484-5x01mL 5x0.1mL
EUR 1205

A4GNT Antibody
MBS7131153-01mL 0.1mL
EUR 270

A4GNT Antibody
MBS7131153-5x01mL 5x0.1mL
EUR 1200

A4GNT Antibody
MBS7120052-005mg 0.05mg
EUR 150

A4GNT Antibody
MBS7120052-01mg 0.1mg
EUR 190

A4GNT Antibody
MBS7120052-5x01mg 5x0.1mg
EUR 845

A4GNT Antibody
MBS851817-01mg 0.1mg
EUR 305

A4GNT Antibody
MBS851817-01mLAF405L 0.1mL(AF405L)
EUR 465

A4GNT Antibody
MBS851817-01mLAF405S 0.1mL(AF405S)
EUR 465

A4GNT Antibody
MBS851817-01mLAF610 0.1mL(AF610)
EUR 465

A4GNT Antibody
MBS851817-01mLAF635 0.1mL(AF635)
EUR 465

A4GNT Antibody
MBS8514491-01mg 0.1mg
EUR 305

A4GNT Antibody
MBS8514491-01mLAF405L 0.1mL(AF405L)
EUR 465

A4GNT Antibody
MBS8514491-01mLAF405S 0.1mL(AF405S)
EUR 465

A4GNT Antibody
MBS8514491-01mLAF610 0.1mL(AF610)
EUR 465

A4GNT Antibody
MBS8514491-01mLAF635 0.1mL(AF635)
EUR 465

A4GNT Antibody
MBS8500281-01mg 0.1mg
EUR 345

A4GNT Antibody
MBS8500281-01mLAF405L 0.1mL(AF405L)
EUR 565

A4GNT Antibody
MBS8500281-01mLAF405S 0.1mL(AF405S)
EUR 565

A4GNT Antibody
MBS8500281-01mLAF610 0.1mL(AF610)
EUR 565

A4GNT Antibody
MBS8500281-01mLAF635 0.1mL(AF635)
EUR 565

A4GNT Antibody
MBS9402842-005mL 0.05mL
EUR 245

A4GNT Antibody
MBS9402842-01mL 0.1mL
EUR 305

A4GNT Antibody
MBS9402842-5x01mL 5x0.1mL
EUR 1230

A4GNT Antibody
MBS9201431-01mL 0.1mL
EUR 415

A4GNT Antibody
MBS9201431-5x01mL 5x0.1mL
EUR 1841

A4GNT Antibody
MBS8581466-01mL 0.1mL
EUR 305

A4GNT Antibody
MBS8581466-01mLAF405L 0.1mL(AF405L)
EUR 465

A4GNT Antibody
MBS8581466-01mLAF405S 0.1mL(AF405S)
EUR 465

A4GNT Antibody
MBS8581466-01mLAF610 0.1mL(AF610)
EUR 465

A4GNT Antibody
MBS8581466-01mLAF635 0.1mL(AF635)
EUR 465

A4GNT Antibody
MBS9605218-01mL 0.1mL
EUR 260

A4GNT Antibody
MBS9605218-02mL 0.2mL
EUR 305

A4GNT Antibody
MBS9605218-5x02mL 5x0.2mL
EUR 1220

A4GNT Antibody
MBS9506010-005mL 0.05mL
EUR 285

A4GNT Antibody
MBS9506010-01mL 0.1mL
EUR 385

A4GNT Antibody
MBS9506010-5x01mL 5x0.1mL
EUR 1590

A4GNT (untagged)-Human alpha-1,4-N-acetylglucosaminyltransferase (A4GNT)
SC304387 10 µg Ask for price

A4GNT Rabbit pAb
A12366 20μL
EUR 262.15

A4GNT Rabbit pAb
A12366-100ul 100 ul
EUR 369.6

A4GNT Rabbit pAb
A12366-200ul 200 ul
EUR 550.8

A4GNT Rabbit pAb
A12366-20ul 20 ul
EUR 219.6

A4GNT Rabbit pAb
A12366-50ul 50 ul
EUR 267.6

A4GNT cDNA Clone
MBS1267881-001mgPlasmid02mLGlycerolStock 0.01mgPlasmid+0.2mLGlycerol-Stock
EUR 200

A4GNT cDNA Clone
MBS1267881-5x001mgPlasmid5x02mLGlycerolStock 5x0.01mgPlasmid+5x0.2mLGlycerol-Stock
EUR 855

A4GNT Rabbit pAb
E45R18995N 50 ul
EUR 297.75

A4GNT Rabbit pAb
E2510891 100ul
EUR 225
Description: Available in various conjugation types.

A4GNT Rabbit pAb
MBS8548199-01mL 0.1mL
EUR 305

A4GNT Rabbit pAb
MBS8548199-01mLAF405L 0.1mL(AF405L)
EUR 565

A4GNT Rabbit pAb
MBS8548199-01mLAF405S 0.1mL(AF405S)
EUR 565

A4GNT Rabbit pAb
MBS8548199-01mLAF610 0.1mL(AF610)
EUR 565

A4GNT Rabbit pAb
MBS8548199-01mLAF635 0.1mL(AF635)
EUR 565

Human A4GNT siRNA
20-abx906234
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  • 15 nmol
  • 30 nmol

A4GNT siRNA (Human)
MBS828787-15nmol 15nmol
EUR 405

A4GNT siRNA (Human)
MBS828787-30nmol 30nmol
EUR 565

A4GNT siRNA (Human)
MBS828787-5x30nmol 5x30nmol
EUR 2450

anti- A4GNT antibody
FNab00015 100µg
EUR 606.3
Description: Antibody raised against A4GNT

A4GNT (GFP-tagged) - Human alpha-1,4-N-acetylglucosaminyltransferase (A4GNT)
RG221256 10 µg Ask for price

A4GNT cloning plasmid
CSB-CL001009HU-10ug 10ug
EUR 279.6
Description: A cloning plasmid for the A4GNT gene.

A4GNT Blocking Peptide
33R-5167 100 ug
EUR 119
Description: A synthetic peptide for use as a blocking control in assays to test for specificity of A4GNT antibody, catalog no. 70R-7408

A4GNT Blocking Peptide
33R-6732 100 ug
EUR 119
Description: A synthetic peptide for use as a blocking control in assays to test for specificity of A4GNT antibody, catalog no. 70R-7409

A4GNT Blocking Peptide
20-abx063854
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  • 1 mg
  • 5 mg

A4GNT Blocking Peptide
DF3762-BP 1mg
EUR 234

A4GNT Blocking Peptide
MBS824283-1mg 1mg
EUR 190

A4GNT Blocking Peptide
MBS824283-5mg 5mg
EUR 345

A4GNT Blocking Peptide
MBS824283-5x5mg 5x5mg
EUR 1465

A4GNT Blocking Peptide
MBS9623935-1mg 1mg
EUR 380

A4GNT Blocking Peptide
MBS9623935-5x1mg 5x1mg
EUR 1650

A4gnt (untagged) - Mouse alpha-1,4-N-acetylglucosaminyltransferase (A4gnt), (10ug)
MC214620 10 µg Ask for price

A4GNT Polyclonal Antibody
A72325
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  • 50 ul
  • 100 ul

A4GNT Polyclonal Antibody
A62026
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  • Ask for price
  • Ask for price
  • 100 µg
  • 20 ul
  • 50 ul
  • 100 ul

A4GNT Conjugated Antibody
C34406 100ul
EUR 476.4

Polyclonal A4GNT Antibody
APG01408G 0.1ml
EUR 580.8
Description: A polyclonal antibody raised in Rabbit that recognizes and binds to Human A4GNT . This antibody is tested and proven to work in the following applications:

A4GNT polyclonal antibody
BS72262 50 ul
EUR 358
Description: 1mg/ml in PBS with 0.02% sodium azide, 50% glycerol, pH7.2

A4GNT Polyclonal Antibody
E912366 100ul
EUR 225
Description: Available in various conjugation types.

A4GNT Polyclonal Antibody
MBS2524940-002mL 0.02mL
EUR 140

A4GNT Polyclonal Antibody
MBS2524940-006mL 0.06mL
EUR 180

A4GNT Polyclonal Antibody
MBS2524940-012mL 0.12mL
EUR 260

A4GNT Polyclonal Antibody
MBS2524940-02mL 0.2mL
EUR 405

A4GNT Polyclonal Antibody
MBS2548051-006mL 0.06mL
EUR 180

A4GNT Polyclonal Antibody
MBS2548051-012mL 0.12mL
EUR 260

A4GNT Polyclonal Antibody
MBS2548051-02mL 0.2mL
EUR 405

A4GNT Polyclonal Antibody
MBS2548051-5x02mL 5x0.2mL
EUR 1725

A4GNT Polyclonal Antibody
MBS2528052-002mL 0.02mL
EUR 140

A4GNT Polyclonal Antibody
MBS2528052-006mL 0.06mL
EUR 180

A4GNT Polyclonal Antibody
MBS2528052-012mL 0.12mL
EUR 260

A4GNT Polyclonal Antibody
MBS2528052-02mL 0.2mL
EUR 405

A4GNT Polyclonal Antibody
MBS2528052-5x02mL 5x0.2mL
EUR 1725

A4GNT Polyclonal Antibody
MBS9132263-002mL 0.02mL
EUR 200

A4GNT Polyclonal Antibody
MBS9132263-005mL 0.05mL
EUR 255

A4GNT Polyclonal Antibody
MBS9132263-01mL 0.1mL
EUR 345

A4GNT Polyclonal Antibody
MBS9132263-02mL 0.2mL
EUR 545

A4GNT Polyclonal Antibody
MBS9132263-5x02mL 5x0.2mL
EUR 2265

A4GNT Polyclonal Antibody
MBS9234051-01mL 0.1mL
EUR 415

A4GNT Polyclonal Antibody
MBS9234051-5x01mL 5x0.1mL
EUR 1841

A4GNT Conjugated Antibody
MBS9445198-01mLAF350 0.1mL(AF350)
EUR 480

A4GNT Conjugated Antibody
MBS9445198-01mLAF405 0.1mL(AF405)
EUR 480

A4GNT Conjugated Antibody
MBS9445198-01mLAF488 0.1mL(AF488)
EUR 480

A4GNT Conjugated Antibody
MBS9445198-01mLAF555 0.1mL(AF555)
EUR 480

A4GNT Conjugated Antibody
MBS9445198-01mLBiotin 0.1mL(Biotin)
EUR 480

A4GNT Polyclonal Antibody
MBS8567258-01mL 0.1mL
EUR 305

A4GNT Polyclonal Antibody
MBS8567258-01mLAF405L 0.1mL(AF405L)
EUR 565

A4GNT Polyclonal Antibody
MBS8567258-01mLAF405S 0.1mL(AF405S)
EUR 565

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