comparison interpro/paso1.xml @ 0:c342ebb50f0b draft default tip

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0:c342ebb50f0b

<tool id="ALaGiFer_1" name="RemoteBlast" version="1.0.0">
    <description>Blast against UniProt/SwissProt database</description>
    <command interpreter="perl">
    paso1.pl $infile $outfile
    </command>

        <inputs>
            <param name="infile" type="data" format="fasta" label="Sequence in Fasta File"/>

          
           </inputs>
<outputs>
<data format="txt" name="outfile"/>
</outputs>

<stdio><exit_code range="1:" level="fatal" description="Error" /></stdio>
    <help>

**What it does**

This tool runs a remote blast against Uniprot/Swissprot database.


**Dependencies**

Bioperl is necessary for running this tool.

#####
Input
#####

Required is a FASTA file containing protein sequences.


######
Output
######

Generates an output text file.


Example Output
--------------
BLASTP 2.2.29+
Reference: Stephen F. Altschul, Thomas L. Madden, Alejandro
A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and
David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new
generation of protein database search programs", Nucleic
Acids Res. 25:3389-3402.


RID: M2E3HVH4014


Database: Non-redundant UniProtKB/SwissProt sequences
           457,803 sequences; 170,956,615 total letters
Query= C08B11.6 CE30856 WBGene00007434  actin   status:Confirmed       
UniProt:Q09443  protein_id:CAA86667.3

Length=418


                                                                   Score     E
Sequences producing significant alignments:                       (Bits)  Value

sp|Q09443.3|ARP6_CAEEL  RecName: Full=Actin-like protein C08B11.6    853   0.0  
sp|Q9D864.2|ARP6_MOUSE  RecName: Full=Actin-related protein 6;...    280   2e-88
sp|Q9GZN1.1|ARP6_HUMAN  RecName: Full=Actin-related protein 6;...    279   5e-88
sp|Q9DEE9.1|ARP6_CHICK  RecName: Full=Actin-related protein 6;...    274   5e-86
sp|P45890.1|ARP6_DROME  RecName: Full=Actin-related protein 6;...    265   1e-82
sp|Q6C982.1|ARP6_YARLI  RecName: Full=Actin-like protein ARP6        232   4e-70
sp|O94241.1|ARP6_SCHPO  RecName: Full=Actin-like protein arp6        228   2e-68
sp|Q7S6X6.1|ARP6_NEUCR  RecName: Full=Actin-related protein 6        212   6e-62
sp|Q5NBI2.1|ARP6_ORYSJ  RecName: Full=Actin-related protein 6 ...    210   3e-61

ALIGNMENTS
>sp|Q09443.3|ARP6_CAEEL RecName: Full=Actin-like protein C08B11.6
Length=418

 Score =   853 bits (2204),  Expect = 0.0
 Identities = 418/418 (100%), Positives = 418/418 (100%), Gaps = 0/418 (0%)

Query  1    MSLTTIIFDNGGHNMKIGTIDSESPRLVPNSIVKAKHEKKRVFVAHEQEECSDKFSLFYV  60
            MSLTTIIFDNGGHNMKIGTIDSESPRLVPNSIVKAKHEKKRVFVAHEQEECSDKFSLFYV
Sbjct  1    MSLTTIIFDNGGHNMKIGTIDSESPRLVPNSIVKAKHEKKRVFVAHEQEECSDKFSLFYV  60

Query  61   RPIERGYVVNWDTQQQIWEKTFGSMDVEASTSRIALTDNNYLIPALPDVSSEILFDYFGF  120
            RPIERGYVVNWDTQQQIWEKTFGSMDVEASTSRIALTDNNYLIPALPDVSSEILFDYFGF
Sbjct  61   RPIERGYVVNWDTQQQIWEKTFGSMDVEASTSRIALTDNNYLIPALPDVSSEILFDYFGF  120

Query  121  TEVHKTSASTLVAKHSNKINNEKCAVVVDSGFSWTTVASFVNGMLIQDSVIRIDVGGKAL  180
            TEVHKTSASTLVAKHSNKINNEKCAVVVDSGFSWTTVASFVNGMLIQDSVIRIDVGGKAL
Sbjct  121  TEVHKTSASTLVAKHSNKINNEKCAVVVDSGFSWTTVASFVNGMLIQDSVIRIDVGGKAL  180

Query  181  TNKLKDWVSYRQLNVSEETYVINECKEDLCFVSQNFDESMKEARNRFQENTTMKRYIMPD  240
            TNKLKDWVSYRQLNVSEETYVINECKEDLCFVSQNFDESMKEARNRFQENTTMKRYIMPD
Sbjct  181  TNKLKDWVSYRQLNVSEETYVINECKEDLCFVSQNFDESMKEARNRFQENTTMKRYIMPD  240


**Galaxy Wrapper Authors**::

    * Laura Entrambasaguas
    * Ginés Almagro
    * Fernando Pérez

    </help>
</tool>