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SIPHT

The bioinformatics project at Harvard University is conducting a wide search for small untranslated RNAs (sRNAs) that regulate several processes such as secretion or virulence in bacteria. The sRNA identification protocol using high-throughput technology (SIPHT) program uses a workflow to automate the search for sRNA encoding-genes for all of the bacterial replicons in the National Center for Biotechnology Information (NCBI) database. The kingdom-wide prediction and annotation of sRNA encoding genes involves a variety of individual programs that are executed in the proper order using Condor DAGMan's capabilities. These involve the prediction of Rho-independent transcriptional terminators, BLAST (Basic Local Alignment Search Tools) comparisons of the inter genetic regions of different replicons and the annotations of any sRNAs that are found.

Execution Profile

Execution times of SIPHT jobs

Job

Count

Mean(s)

Variance

Blast_candidate

1

5.8

0

Blast_paralogues

1

4.5

0

Blast_QRNA

1

1344.88

0

Blast_synteny

1

33

0

FFN_parse

1

1.4

0

Findterm

1

975.16

0

Patser

17

1.3

0.19

Patser_concate

1

0.01

0

RNAMotif

1

44

0

SRNA

1

306.53

0

SRNA_annotate

1

1.9

0

Transterm

1

32

0

Sizes of SIPHT data items

File Type

Count

Mean(MB)

Variance

alphabet

1

1.5e-05

0

blasta

1

0.75

0

BLAST_*

1

0.0081

0

BLAST_Out

1

2

0

blast_paralogues.out

1

0.003

0

BLAST_sorted.out

1

4.3

0

blast_synteny.out

1

0.011

0

eqrna

1

0.91

0

findterm.out

1

0.00013

0

IGR_Partners

934

0.28

0.098

TFBS_matrices

18

0.0097

0.0014

  • .ffn

1

3.9

0

  • .fna

1

4.3

0

  • .gbk

1

10

0

  • _paralogues.txt

1

1.2

0

  • _parsed.ffn

1

0.83

0

  • _PatserOut.txt

1

0.11

0

  • .ptt

1

0.31

0

  • _QRNA.txt

1

0.75

0

  • _sRNA.out

1

0.098

0

  • _sRNA.out_annotated

1

0.2

0

  • _synteny.txt

1

1.3

0

  • _term_cand_nonredund

1

0.37

0

  • _term.txt

1

23

0

OutBlastParsed

1

0.48

0

OutCandidates

3

0.26

0.0076

patser.in

1

1.3e-05

0

patser.out

17

0.0067

2e-05

QRNA_out

1

0.0093

0

RNAMofficial_desc.txt

1

0.017

0

rnamotif.out

1

1

0

rna.ps

1

0.0027

0

Seq_known_sRNAs_IGRs

1

0.16

0

Seq_*

1

0.077

0

srna_annotate.out

1

0.65

0

sRNAPredict.in

1

0.0011

0

transterm.err

1

9.2e-05

0

transterm.out

1

0.41

0

vienna_index_tmp

1

6.8

0

vienna_input_tmp

1

4.7

0

vienna_output

1

11

0

xdformat

1

0.36

0

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