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 Protein Homology/analogY Recognition Engine V 2.0


 

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Batch processing

The batch processing feature now permits users to submit more than one sequence to Phyre by uploading a file of sequences in FASTA format. By default, users have a limit of 100 sequences in a batch. If you require this limit to be raised, please contact me (Lawrence Kelley)

Batch jobs are processed in the background on free computing power as it becomes available. Thus, batch jobs will often take longer than individually submitted jobs, but this is necessary to allow a fair ditribution of computing resources to all Phyre users. In addition, users are only permitted to have one active batch job at a time. Once your batch job is completed, or stopped by you, you will be permitted to submit a new batch job.

Finally, it should be noted that batch sequences can currently only run in 'normal' mode and not 'intensive' mode to conserve computing resources.

Format of sequences

>P31946
MTMDKSELVQKAKLAEQAERYDDMAAAMKAVTEQGHELSNEERNLLSVAYKNVVGARRSSWRVISSIEQKTERNEKKQQMGKEYREKIEAELQ
DICNDVLELLDKYLIPNATQPESKVFYLKMKGDYFRYLSEVASGDNKQTTVSNSQQAYQEAFEISKKEMQPTHPIRLGLALNFSV
FYYEILNSPEKACSLAKTAFDEAIAELDTLNEESYKDSTLIMQLLRDNLTLWTSENQGDEGDAGEGEN
>P62258
MDDREDLVYQAKLAEQAERYDEMVESMKKVAGMDVELTVEERNLLSVAYKNVIGARRASWRIISSIEQKEENKGGEDKLKMIREYRQMVETEL
KLICCDILDVLDKHLIPAANTGESKVFYYKMKGDYHRYLAEFATGNDRKEAAENSLVAYKAASDIAMTELPPTHPIRLGLALNFS
VFYYEILNSPDRACRLAKAAFDDAIAELDTLSEESYKDSTLIMQLLRDNLTLWTSDMQGDGEEQNKEALQDVEDENQ
>Q04917
MGDREQLLQRARLAEQAERYDDMASAMKAVTELNEPLSNEDRNLLSVAYKNVVGARRSSWRVISSIEQKTMADGNEKKLEKVKAYREKIEKEL
ETVCNDVLSLLDKFLIKNCNDFQYESKVFYLKMKGDYYRYLAEVASGEKKNSVVEASEAAYKEAFEISKEQMQPTHPIRLGLALN
FSVFYYEIQNAPEQACLLAKQAFDDAIAELDTLNEDSYKDSTLIMQLLRDNLTLWTSDQQDEEAGEGN
>P61981
MVDREQLVQKARLAEQAERYDDMAAAMKNVTELNEPLSNEERNLLSVAYKNVVGARRSSWRVISSIEQKTSADGNEKKIEMVRAYREKIEKE
LEAVCQDVLSLLDNYLIKNCSETQYESKVFYLKMKGDYYRYLAEVATGEKRATVVESSEKAYSEAHEISKEHMQPTHPIRLGLALN
YSVFYYEIQNAPEQACHLAKTAFDDAIAELDTLNEDSYKDSTLIMQLLRDNLTLWTSDQQDDDGGEGNN

Sequences do not need to have carriage returns after a certain number of residues. Carriage returns and spaces in the sequence are ignored. Simply ensure each sequence has an associated identifier preceded by a '>' character. Upon uploading your file, the Phyre server will display how it has interpreted the data before you confirm job submission. Please ensure your sequences have been parsed correctly before confirming final submission.



Phyre is for non-commercial use only

Commercial users please contact Michael Sternberg

Please cite: The Phyre2 web portal for protein modeling, prediction and analysis
Kelley LA et al. Nature Protocols 10, 845-858 (2015) [paper] [Citation link]
 
© Structural Bioinformatics Group, Imperial College, London
Lawrence Kelley, Michael Sternberg 
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